Sample records for transition path ensemble
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Li, Wenjin
2018-02-28
Transition path ensemble consists of reactive trajectories and possesses all the information necessary for the understanding of the mechanism and dynamics of important condensed phase processes. However, quantitative description of the properties of the transition path ensemble is far from being established. Here, with numerical calculations on a model system, the equipartition terms defined in thermal equilibrium were for the first time estimated in the transition path ensemble. It was not surprising to observe that the energy was not equally distributed among all the coordinates. However, the energies distributed on a pair of conjugated coordinates remained equal. Higher energies were observed to be distributed on several coordinates, which are highly coupled to the reaction coordinate, while the rest were almost equally distributed. In addition, the ensemble-averaged energy on each coordinate as a function of time was also quantified. These quantitative analyses on energy distributions provided new insights into the transition path ensemble.
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A benchmark for reaction coordinates in the transition path ensemble
2016-01-01
The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. PMID:27059559
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Statistical Analysis of the First Passage Path Ensemble of Jump Processes
NASA Astrophysics Data System (ADS)
von Kleist, Max; Schütte, Christof; Zhang, Wei
2018-02-01
The transition mechanism of jump processes between two different subsets in state space reveals important dynamical information of the processes and therefore has attracted considerable attention in the past years. In this paper, we study the first passage path ensemble of both discrete-time and continuous-time jump processes on a finite state space. The main approach is to divide each first passage path into nonreactive and reactive segments and to study them separately. The analysis can be applied to jump processes which are non-ergodic, as well as continuous-time jump processes where the waiting time distributions are non-exponential. In the particular case that the jump processes are both Markovian and ergodic, our analysis elucidates the relations between the study of the first passage paths and the study of the transition paths in transition path theory. We provide algorithms to numerically compute statistics of the first passage path ensemble. The computational complexity of these algorithms scales with the complexity of solving a linear system, for which efficient methods are available. Several examples demonstrate the wide applicability of the derived results across research areas.
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Bhatt, Divesh; Zuckerman, Daniel M.
2010-01-01
We performed “weighted ensemble” path–sampling simulations of adenylate kinase, using several semi–atomistic protein models. The models have an all–atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single–processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semi–atomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways. PMID:21660120
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Ovchinnikov, Victor; Karplus, Martin
2012-07-26
The popular targeted molecular dynamics (TMD) method for generating transition paths in complex biomolecular systems is revisited. In a typical TMD transition path, the large-scale changes occur early and the small-scale changes tend to occur later. As a result, the order of events in the computed paths depends on the direction in which the simulations are performed. To identify the origin of this bias, and to propose a method in which the bias is absent, variants of TMD in the restraint formulation are introduced and applied to the complex open ↔ closed transition in the protein calmodulin. Due to the global best-fit rotation that is typically part of the TMD method, the simulated system is guided implicitly along the lowest-frequency normal modes, until the large spatial scales associated with these modes are near the target conformation. The remaining portion of the transition is described progressively by higher-frequency modes, which correspond to smaller-scale rearrangements. A straightforward modification of TMD that avoids the global best-fit rotation is the locally restrained TMD (LRTMD) method, in which the biasing potential is constructed from a number of TMD potentials, each acting on a small connected portion of the protein sequence. With a uniform distribution of these elements, transition paths that lack the length-scale bias are obtained. Trajectories generated by steered MD in dihedral angle space (DSMD), a method that avoids best-fit rotations altogether, also lack the length-scale bias. To examine the importance of the paths generated by TMD, LRTMD, and DSMD in the actual transition, we use the finite-temperature string method to compute the free energy profile associated with a transition tube around a path generated by each algorithm. The free energy barriers associated with the paths are comparable, suggesting that transitions can occur along each route with similar probabilities. This result indicates that a broad ensemble of paths needs to be calculated to obtain a full description of conformational changes in biomolecules. The breadth of the contributing ensemble suggests that energetic barriers for conformational transitions in proteins are offset by entropic contributions that arise from a large number of possible paths.
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Edwards, James P; Gerber, Urs; Schubert, Christian; Trejo, Maria Anabel; Weber, Axel
2018-04-01
We introduce two integral transforms of the quantum mechanical transition kernel that represent physical information about the path integral. These transforms can be interpreted as probability distributions on particle trajectories measuring respectively the relative contribution to the path integral from paths crossing a given spatial point (the hit function) and the likelihood of values of the line integral of the potential along a path in the ensemble (the path-averaged potential).
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NASA Astrophysics Data System (ADS)
Edwards, James P.; Gerber, Urs; Schubert, Christian; Trejo, Maria Anabel; Weber, Axel
2018-04-01
We introduce two integral transforms of the quantum mechanical transition kernel that represent physical information about the path integral. These transforms can be interpreted as probability distributions on particle trajectories measuring respectively the relative contribution to the path integral from paths crossing a given spatial point (the hit function) and the likelihood of values of the line integral of the potential along a path in the ensemble (the path-averaged potential).
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Synoptic Factors Affecting Structure Predictability of Hurricane Alex (2016)
NASA Astrophysics Data System (ADS)
Gonzalez-Aleman, J. J.; Evans, J. L.; Kowaleski, A. M.
2016-12-01
On January 7, 2016, a disturbance formed over the western North Atlantic basin. After undergoing tropical transition, the system became the first hurricane of 2016 - and the first North Atlantic hurricane to form in January since 1938. Already an extremely rare hurricane event, Alex then underwent extratropical transition [ET] just north of the Azores Islands. We examine the factors affecting Alex's structural evolution through a new technique called path-clustering. In this way, 51 ensembles from the European Centre for Medium-Range Weather Forecasts Ensemble Prediction System (ECMWF-EPS) are grouped based on similarities in the storm's path through the Cyclone Phase Space (CPS). The differing clusters group various possible scenarios of structural development represented in the ensemble forecasts. As a result, it is possible to shed light on the role of the synoptic scale in changing the structure of this hurricane in the midlatitudes through intercomparison of the most "realistic" forecast of the evolution of Alex and the other physically plausible modes of its development.
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Quantum Gibbs ensemble Monte Carlo
DOE Office of Scientific and Technical Information (OSTI.GOV)
Fantoni, Riccardo, E-mail: rfantoni@ts.infn.it; Moroni, Saverio, E-mail: moroni@democritos.it
We present a path integral Monte Carlo method which is the full quantum analogue of the Gibbs ensemble Monte Carlo method of Panagiotopoulos to study the gas-liquid coexistence line of a classical fluid. Unlike previous extensions of Gibbs ensemble Monte Carlo to include quantum effects, our scheme is viable even for systems with strong quantum delocalization in the degenerate regime of temperature. This is demonstrated by an illustrative application to the gas-superfluid transition of {sup 4}He in two dimensions.
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Sampling the kinetic pathways of a micelle fusion and fission transition.
Pool, René; Bolhuis, Peter G
2007-06-28
The mechanism and kinetics of micellar breakup and fusion in a dilute solution of a model surfactant are investigated by path sampling techniques. Analysis of the path ensemble gives insight in the mechanism of the transition. For larger, less stable micelles the fission/fusion occurs via a clear neck formation, while for smaller micelles the mechanism is more direct. In addition, path analysis yields an appropriate order parameter to evaluate the fusion and fission rate constants using stochastic transition interface sampling. For the small, stable micelle (50 surfactants) the computed fission rate constant is a factor of 10 lower than the fusion rate constant. The procedure opens the way for accurate calculation of free energy and kinetics for, e.g., membrane fusion, and wormlike micelle endcap formation.
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Graph transformation method for calculating waiting times in Markov chains.
Trygubenko, Semen A; Wales, David J
2006-06-21
We describe an exact approach for calculating transition probabilities and waiting times in finite-state discrete-time Markov processes. All the states and the rules for transitions between them must be known in advance. We can then calculate averages over a given ensemble of paths for both additive and multiplicative properties in a nonstochastic and noniterative fashion. In particular, we can calculate the mean first-passage time between arbitrary groups of stationary points for discrete path sampling databases, and hence extract phenomenological rate constants. We present a number of examples to demonstrate the efficiency and robustness of this approach.
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Improved transition path sampling methods for simulation of rare events
NASA Astrophysics Data System (ADS)
Chopra, Manan; Malshe, Rohit; Reddy, Allam S.; de Pablo, J. J.
2008-04-01
The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.
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A path integral approach to the full Dicke model with dipole-dipole interaction
NASA Astrophysics Data System (ADS)
Aparicio Alcalde, M.; Stephany, J.; Svaiter, N. F.
2011-12-01
We consider the full Dicke spin-boson model composed by a single bosonic mode and an ensemble of N identical two-level atoms with different couplings for the resonant and anti-resonant interaction terms, and incorporate a dipole-dipole interaction between the atoms. Assuming that the system is in thermal equilibrium with a reservoir at temperature β-1, we compute the free energy in the thermodynamic limit N → ∞ in the saddle-point approximation to the path integral and determine the critical temperature for the super-radiant phase transition. In the zero temperature limit, we recover the critical coupling of the quantum phase transition, presented in the literature.
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Zheng, Jingjing; Truhlar, Donald G
2012-01-01
Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.
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Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus' theory.
Tiwari, Ambuj; Ensing, Bernd
2016-12-22
Outer sphere electron transfer between two ions in aqueous solution is a rare event on the time scale of first principles molecular dynamics simulations. We have used transition path sampling to generate an ensemble of reactive trajectories of the self-exchange reaction between a pair of Ru 2+ and Ru 3+ ions in water. To distinguish between the reactant and product states, we use as an order parameter the position of the maximally localised Wannier center associated with the transferring electron. This allows us to align the trajectories with respect to the moment of barrier crossing and compute statistical averages over the path ensemble. We compare our order parameter with two typical reaction coordinates used in applications of Marcus theory of electron transfer: the vertical gap energy and the solvent electrostatic potential at the ions.
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H theorem for generalized entropic forms within a master-equation framework
NASA Astrophysics Data System (ADS)
Casas, Gabriela A.; Nobre, Fernando D.; Curado, Evaldo M. F.
2016-03-01
The H theorem is proven for generalized entropic forms, in the case of a discrete set of states. The associated probability distributions evolve in time according to a master equation, for which the corresponding transition rates depend on these entropic forms. An important equation describing the time evolution of the transition rates and probabilities in such a way as to drive the system towards an equilibrium state is found. In the particular case of Boltzmann-Gibbs entropy, it is shown that this equation is satisfied in the microcanonical ensemble only for symmetric probability transition rates, characterizing a single path to the equilibrium state. This equation fulfils the proof of the H theorem for generalized entropic forms, associated with systems characterized by complex dynamics, e.g., presenting nonsymmetric probability transition rates and more than one path towards the same equilibrium state. Some examples considering generalized entropies of the literature are discussed, showing that they should be applicable to a wide range of natural phenomena, mainly those within the realm of complex systems.
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Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
Seyler, Sean L.; Kumar, Avishek; Thorpe, M. F.; Beckstein, Oliver
2015-01-01
Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that the geometry-based FRODA occasionally sampled the pathway space of force field-based DIMS MD. For the AdK transition, the new concept of a Hausdorff-pair map enabled us to extract the molecular structural determinants responsible for differences in pathways, namely a set of conserved salt bridges whose charge-charge interactions are fully modelled in DIMS MD but not in FRODA. PSA has the potential to enhance our understanding of transition path sampling methods, validate them, and to provide a new approach to analyzing conformational transitions. PMID:26488417
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Molloy, Kevin; Shehu, Amarda
2013-01-01
Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.
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Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water
Juraszek, Jarek; Bolhuis, Peter G.
2008-01-01
We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the protein maintains its compact configuration, while a (de)increase of secondary structure is observed. The calculated folding rate agrees reasonably with experiment, while the unfolding rate is 10 times higher. We discuss possible origins for this mismatch. We recomputed the rates with the forward flux sampling method, and found a discrepancy of four orders of magnitude, probably caused by the method's higher sensitivity to the choice of order parameter with respect to transition interface sampling. Finally, we used the previously computed transition path-sampling ensemble to screen combinations of many order parameters for the best model of the reaction coordinate by employing likelihood maximization. We found that a combination of the root mean-square deviation of the helix and of the entire protein was, of the set of tried order parameters, the one that best describes the reaction coordination. PMID:18676648
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Free energy landscape from path-sampling: application to the structural transition in LJ38
NASA Astrophysics Data System (ADS)
Adjanor, G.; Athènes, M.; Calvo, F.
2006-09-01
We introduce a path-sampling scheme that allows equilibrium state-ensemble averages to be computed by means of a biased distribution of non-equilibrium paths. This non-equilibrium method is applied to the case of the 38-atom Lennard-Jones atomic cluster, which has a double-funnel energy landscape. We calculate the free energy profile along the Q4 bond orientational order parameter. At high or moderate temperature the results obtained using the non-equilibrium approach are consistent with those obtained using conventional equilibrium methods, including parallel tempering and Wang-Landau Monte Carlo simulations. At lower temperatures, the non-equilibrium approach becomes more efficient in exploring the relevant inherent structures. In particular, the free energy agrees with the predictions of the harmonic superposition approximation.
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NASA Astrophysics Data System (ADS)
Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik
2016-08-01
Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.
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2013-01-01
Background Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. Methods We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Results and conclusions Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers. PMID:24565158
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Girsanov reweighting for path ensembles and Markov state models
NASA Astrophysics Data System (ADS)
Donati, L.; Hartmann, C.; Keller, B. G.
2017-06-01
The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor "on the fly" during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics.
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Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways
Wu, Dongsheng; Fajer, Mikolai I.; Cao, Liaoran; Cheng, Xiaolin; Yang, Wei
2016-01-01
Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this mini presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634
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Water evaporation: a transition path sampling study.
Varilly, Patrick; Chandler, David
2013-02-07
We use transition path sampling to study evaporation in the SPC/E model of liquid water. On the basis of thousands of evaporation trajectories, we characterize the members of the transition state ensemble (TSE), which exhibit a liquid-vapor interface with predominantly negative mean curvature at the site of evaporation. We also find that after evaporation is complete, the distributions of translational and angular momenta of the evaporated water are Maxwellian with a temperature equal to that of the liquid. To characterize the evaporation trajectories in their entirety, we find that it suffices to project them onto just two coordinates: the distance of the evaporating molecule to the instantaneous liquid-vapor interface and the velocity of the water along the average interface normal. In this projected space, we find that the TSE is well-captured by a simple model of ballistic escape from a deep potential well, with no additional barrier to evaporation beyond the cohesive strength of the liquid. Equivalently, they are consistent with a near-unity probability for a water molecule impinging upon a liquid droplet to condense. These results agree with previous simulations and with some, but not all, recent experiments.
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Effects of a mutation on the folding mechanism of a beta-hairpin.
Juraszek, Jarek; Bolhuis, Peter G
2009-12-17
The folding mechanism of a protein is determined by its primary sequence. Yet, how the mechanism is changed by a mutation is still poorly understood, even for basic secondary structures such as beta-hairpins. We perform an extensive simulation study of the effects of mutating the GB1 beta-hairpin into Trpzip4 (Y5W, F12W, V14W) on the folding mechanism. While Trpzip4 has a much more stable native state due to very strong hydrophobic interactions of the side chains, its folding rate does not differ significantly from the wild type beta-hairpin. We sample the free-energy landscapes of both hairpins with Replica Exchange Molecular Dynamics (REMD) and identify the four (meta)stable states (U, H, F, and N). Using Transition Path Sampling (TPS), we then harvest ensembles of unbiased pathways between the H and F states and between the F and N states to investigate the unbiased folding mechanisms. In both hairpins, the hydrophobic collapse (U-H) is followed by the middle hydrogen bond formation (H-F), and finally a closing of the strands in a zipper-like fashion (F-N). For the Trpzip4, the path ensembles indicate that the final F-N step is much more difficult than for GB1 and involves partial unfolding, rezipping of hydrogen bonds, and rearrangement of the Trp-14 side chain. For the rate-limiting (H-F) step, the path ensembles show that in GB1 desolvation and strand closure go hand in hand, while in Trpzip4 desolvation is decoupled from strand closure. Nevertheless, likelihood maximization shows that the reaction coordinate for both hairpins remains the interstrand distance. We conclude that the folding mechanism of both hairpins is a combination of hydrophobic collapse and zipping of hydrogen bonds but that the zipper mechanism is more visible in Trpzip4. A major difference between the two hairpins is that in the transition state of the rate-limiting step for Trpzip4 one tryptophan is exposed to the solvent due to steric hindrance, making the folding mechanism more complex and leading to an increased F-N barrier. Thus, our results show in atomistic detail how a mutation leads to a different folding mechanism and results in a more frustrated folding free-energy landscape.
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Tunable ion-photon entanglement in an optical cavity.
Stute, A; Casabone, B; Schindler, P; Monz, T; Schmidt, P O; Brandstätter, B; Northup, T E; Blatt, R
2012-05-23
Proposed quantum networks require both a quantum interface between light and matter and the coherent control of quantum states. A quantum interface can be realized by entangling the state of a single photon with the state of an atomic or solid-state quantum memory, as demonstrated in recent experiments with trapped ions, neutral atoms, atomic ensembles and nitrogen-vacancy spins. The entangling interaction couples an initial quantum memory state to two possible light-matter states, and the atomic level structure of the memory determines the available coupling paths. In previous work, the transition parameters of these paths determined the phase and amplitude of the final entangled state, unless the memory was initially prepared in a superposition state (a step that requires coherent control). Here we report fully tunable entanglement between a single (40)Ca(+) ion and the polarization state of a single photon within an optical resonator. Our method, based on a bichromatic, cavity-mediated Raman transition, allows us to select two coupling paths and adjust their relative phase and amplitude. The cavity setting enables intrinsically deterministic, high-fidelity generation of any two-qubit entangled state. This approach is applicable to a broad range of candidate systems and thus is a promising method for distributing information within quantum networks.
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Path planning in uncertain flow fields using ensemble method
NASA Astrophysics Data System (ADS)
Wang, Tong; Le Maître, Olivier P.; Hoteit, Ibrahim; Knio, Omar M.
2016-10-01
An ensemble-based approach is developed to conduct optimal path planning in unsteady ocean currents under uncertainty. We focus our attention on two-dimensional steady and unsteady uncertain flows, and adopt a sampling methodology that is well suited to operational forecasts, where an ensemble of deterministic predictions is used to model and quantify uncertainty. In an operational setting, much about dynamics, topography, and forcing of the ocean environment is uncertain. To address this uncertainty, the flow field is parametrized using a finite number of independent canonical random variables with known densities, and the ensemble is generated by sampling these variables. For each of the resulting realizations of the uncertain current field, we predict the path that minimizes the travel time by solving a boundary value problem (BVP), based on the Pontryagin maximum principle. A family of backward-in-time trajectories starting at the end position is used to generate suitable initial values for the BVP solver. This allows us to examine and analyze the performance of the sampling strategy and to develop insight into extensions dealing with general circulation ocean models. In particular, the ensemble method enables us to perform a statistical analysis of travel times and consequently develop a path planning approach that accounts for these statistics. The proposed methodology is tested for a number of scenarios. We first validate our algorithms by reproducing simple canonical solutions, and then demonstrate our approach in more complex flow fields, including idealized, steady and unsteady double-gyre flows.
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Simulation studies of the fidelity of biomolecular structure ensemble recreation
NASA Astrophysics Data System (ADS)
Lätzer, Joachim; Eastwood, Michael P.; Wolynes, Peter G.
2006-12-01
We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm using input from "gold standard" reference ensembles that were first generated with a Gō-like Hamiltonian having nonpairwise additive terms. A set of low resolution data, which function as the "experimental" ϕ values, were first constructed from this reference ensemble. The resulting ϕ values were then treated as one would treat laboratory experimental data and were used as input in the replica reconstruction algorithm. The resulting ensembles of structures obtained by the replica algorithm were compared to the gold standard reference ensemble, from which those "data" were, in fact, obtained. It is found that for a unimodal transition state ensemble with a low barrier, the multiple replica algorithm does recreate the reference ensemble fairly successfully when no experimental error is assumed. The Kolmogorov-Smirnov test as well as principal component analysis show that the overlap of the recovered and reference ensembles is significantly enhanced when multiple replicas are used. Reduction of the multiple replica ensembles by clustering successfully yields subensembles with close similarity to the reference ensembles. On the other hand, for a high barrier transition state with two distinct transition state ensembles, the single replica algorithm only samples a few structures of one of the reference ensemble basins. This is due to the fact that the ϕ values are intrinsically ensemble averaged quantities. The replica algorithm with multiple copies does sample both reference ensemble basins. In contrast to the single replica case, the multiple replicas are constrained to reproduce the average ϕ values, but allow fluctuations in ϕ for each individual copy. These fluctuations facilitate a more faithful sampling of the reference ensemble basins. Finally, we test how robustly the reconstruction algorithm can function by introducing errors in ϕ comparable in magnitude to those suggested by some authors. In this circumstance we observe that the chances of ensemble recovery with the replica algorithm are poor using a single replica, but are improved when multiple copies are used. A multimodal transition state ensemble, however, turns out to be more sensitive to large errors in ϕ (if appropriately gauged) and attempts at successful recreation of the reference ensemble with simple replica algorithms can fall short.
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Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Matsunaga, Yasuhiro; Fujisaki, Hiroshi; Terada, Tohru; Furuta, Tadaomi; Moritsugu, Kei; Kidera, Akinori
2012-01-01
Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme. PMID:22685395
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NASA Astrophysics Data System (ADS)
Semenova, Nadezhda I.; Rybalova, Elena V.; Strelkova, Galina I.; Anishchenko, Vadim S.
2017-03-01
We consider in detail similarities and differences of the "coherence-incoherence" transition in ensembles of nonlocally coupled chaotic discrete-time systems with nonhyperbolic and hyperbolic attractors. As basic models we employ the Hénon map and the Lozi map. We show that phase and amplitude chimera states appear in a ring of coupled Hénon maps, while no chimeras are observed in an ensemble of coupled Lozi maps. In the latter, the transition to spatio-temporal chaos occurs via solitary states. We present numerical results for the coupling function which describes the impact of neighboring oscillators on each partial element of an ensemble with nonlocal coupling. Varying the coupling strength we analyze the evolution of the coupling function and discuss in detail its role in the "coherence-incoherence" transition in the ensembles of Hénon and Lozi maps.
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NASA Technical Reports Server (NTRS)
MIittman, David S
2011-01-01
Ensemble is an open architecture for the development, integration, and deployment of mission operations software. Fundamentally, it is an adaptation of the Eclipse Rich Client Platform (RCP), a widespread, stable, and supported framework for component-based application development. By capitalizing on the maturity and availability of the Eclipse RCP, Ensemble offers a low-risk, politically neutral path towards a tighter integration of operations tools. The Ensemble project is a highly successful, ongoing collaboration among NASA Centers. Since 2004, the Ensemble project has supported the development of mission operations software for NASA's Exploration Systems, Science, and Space Operations Directorates.
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On the structure and phase transitions of power-law Poissonian ensembles
NASA Astrophysics Data System (ADS)
Eliazar, Iddo; Oshanin, Gleb
2012-10-01
Power-law Poissonian ensembles are Poisson processes that are defined on the positive half-line, and that are governed by power-law intensities. Power-law Poissonian ensembles are stochastic objects of fundamental significance; they uniquely display an array of fractal features and they uniquely generate a span of important applications. In this paper we apply three different methods—oligarchic analysis, Lorenzian analysis and heterogeneity analysis—to explore power-law Poissonian ensembles. The amalgamation of these analyses, combined with the topology of power-law Poissonian ensembles, establishes a detailed and multi-faceted picture of the statistical structure and the statistical phase transitions of these elemental ensembles.
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Transition from normal to ballistic diffusion in a one-dimensional impact system
NASA Astrophysics Data System (ADS)
Livorati, André L. P.; Kroetz, Tiago; Dettmann, Carl P.; Caldas, Iberê L.; Leonel, Edson D.
2018-03-01
We characterize a transition from normal to ballistic diffusion in a bouncing ball dynamics. The system is composed of a particle, or an ensemble of noninteracting particles, experiencing elastic collisions with a heavy and periodically moving wall under the influence of a constant gravitational field. The dynamics lead to a mixed phase space where chaotic orbits have a free path to move along the velocity axis, presenting a normal diffusion behavior. Depending on the control parameter, one can observe the presence of featured resonances, known as accelerator modes, that lead to a ballistic growth of velocity. Through statistical and numerical analysis of the velocity of the particle, we are able to characterize a transition between the two regimes, where transport properties were used to characterize the scenario of the ballistic regime. Also, in an analysis of the probability of an orbit to reach an accelerator mode as a function of the velocity, we observe a competition between the normal and ballistic transport in the midrange velocity.
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Transition from normal to ballistic diffusion in a one-dimensional impact system.
Livorati, André L P; Kroetz, Tiago; Dettmann, Carl P; Caldas, Iberê L; Leonel, Edson D
2018-03-01
We characterize a transition from normal to ballistic diffusion in a bouncing ball dynamics. The system is composed of a particle, or an ensemble of noninteracting particles, experiencing elastic collisions with a heavy and periodically moving wall under the influence of a constant gravitational field. The dynamics lead to a mixed phase space where chaotic orbits have a free path to move along the velocity axis, presenting a normal diffusion behavior. Depending on the control parameter, one can observe the presence of featured resonances, known as accelerator modes, that lead to a ballistic growth of velocity. Through statistical and numerical analysis of the velocity of the particle, we are able to characterize a transition between the two regimes, where transport properties were used to characterize the scenario of the ballistic regime. Also, in an analysis of the probability of an orbit to reach an accelerator mode as a function of the velocity, we observe a competition between the normal and ballistic transport in the midrange velocity.
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NASA Astrophysics Data System (ADS)
Torre, Emanuele G. Dalla; Diehl, Sebastian; Lukin, Mikhail D.; Sachdev, Subir; Strack, Philipp
2013-02-01
We investigate nonequilibrium phase transitions for driven atomic ensembles interacting with a cavity mode and coupled to a Markovian dissipative bath. In the thermodynamic limit and at low frequencies, we show that the distribution function of the photonic mode is thermal, with an effective temperature set by the atom-photon interaction strength. This behavior characterizes the static and dynamic critical exponents of the associated superradiance transition. Motivated by these considerations, we develop a general Keldysh path-integral approach that allows us to study physically relevant nonlinearities beyond the idealized Dicke model. Using standard diagrammatic techniques, we take into account the leading-order corrections due to the finite number N of atoms. For finite N, the photon mode behaves as a damped classical nonlinear oscillator at finite temperature. For the atoms, we propose a Dicke action that can be solved for any N and correctly captures the atoms’ depolarization due to dissipative dephasing.
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Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.
Singh, Richa; Bansal, Rohit; Rathore, Anurag Singh; Goel, Gaurav
2017-04-25
Earliest events in the aggregation process, such as single molecule reconfiguration, are extremely important and the most difficult to characterize in experiments. To this end, we have used well-tempered bias exchange metadynamics simulations to determine the equilibrium ensembles of an insulin molecule under amyloidogenic conditions of low pH and high temperature. A bin-based clustering method that uses statistics accumulated in bias exchange metadynamics trajectories was employed to construct a detailed thermodynamic and kinetic model of insulin folding. The highest lifetime, lowest free-energy ensemble identified consisted of native conformations adopted by a folded insulin monomer in solution, namely, the R-, the R f -, and the T-states of insulin. The lowest free-energy structure had a root mean square deviation of only 0.15 nm from native x-ray structure. The second longest-lived metastable state was an unfolded, compact monomer with little similarity to the native structure. We have identified three additional long-lived, metastable states from the bin-based model. We then carried out an exhaustive structural characterization of metastable states on the basis of tertiary contact maps and per-residue accessible surface areas. We have also determined the lowest free-energy path between two longest-lived metastable states and confirm earlier findings of non-two-state folding for insulin through a folding intermediate. The ensemble containing the monomeric intermediate retained 58% of native hydrophobic contacts, however, accompanied by a complete loss of native secondary structure. We have discussed the relative importance of nativelike versus nonnative tertiary contacts for the folding transition. We also provide a simple measure to determine the importance of an individual residue for folding transition. Finally, we have compared and contrasted this intermediate with experimental data obtained in spectroscopic, crystallographic, and calorimetric measurements during early stages of insulin aggregation. We have also determined stability of monomeric insulin by incubation at a very low concentration to isolate protein-protein interaction effects. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Nonequilibrium umbrella sampling in spaces of many order parameters
NASA Astrophysics Data System (ADS)
Dickson, Alex; Warmflash, Aryeh; Dinner, Aaron R.
2009-02-01
We recently introduced an umbrella sampling method for obtaining nonequilibrium steady-state probability distributions projected onto an arbitrary number of coordinates that characterize a system (order parameters) [A. Warmflash, P. Bhimalapuram, and A. R. Dinner, J. Chem. Phys. 127, 154112 (2007)]. Here, we show how our algorithm can be combined with the image update procedure from the finite-temperature string method for reversible processes [E. Vanden-Eijnden and M. Venturoli, "Revisiting the finite temperature string method for calculation of reaction tubes and free energies," J. Chem. Phys. (in press)] to enable restricted sampling of a nonequilibrium steady state in the vicinity of a path in a many-dimensional space of order parameters. For the study of transitions between stable states, the adapted algorithm results in improved scaling with the number of order parameters and the ability to progressively refine the regions of enforced sampling. We demonstrate the algorithm by applying it to a two-dimensional model of driven Brownian motion and a coarse-grained (Ising) model for nucleation under shear. It is found that the choice of order parameters can significantly affect the convergence of the simulation; local magnetization variables other than those used previously for sampling transition paths in Ising systems are needed to ensure that the reactive flux is primarily contained within a tube in the space of order parameters. The relation of this method to other algorithms that sample the statistics of path ensembles is discussed.
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Path-integral simulation of solids.
Herrero, C P; Ramírez, R
2014-06-11
The path-integral formulation of the statistical mechanics of quantum many-body systems is described, with the purpose of introducing practical techniques for the simulation of solids. Monte Carlo and molecular dynamics methods for distinguishable quantum particles are presented, with particular attention to the isothermal-isobaric ensemble. Applications of these computational techniques to different types of solids are reviewed, including noble-gas solids (helium and heavier elements), group-IV materials (diamond and elemental semiconductors), and molecular solids (with emphasis on hydrogen and ice). Structural, vibrational, and thermodynamic properties of these materials are discussed. Applications also include point defects in solids (structure and diffusion), as well as nuclear quantum effects in solid surfaces and adsorbates. Different phenomena are discussed, as solid-to-solid and orientational phase transitions, rates of quantum processes, classical-to-quantum crossover, and various finite-temperature anharmonic effects (thermal expansion, isotopic effects, electron-phonon interactions). Nuclear quantum effects are most remarkable in the presence of light atoms, so that especial emphasis is laid on solids containing hydrogen as a constituent element or as an impurity.
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Yang, Li; Sun, Rui; Hase, William L
2011-11-08
In a previous study (J. Chem. Phys.2008, 129, 094701) it was shown that for a large molecule, with a total energy much greater than its barrier for decomposition and whose vibrational modes are harmonic oscillators, the expressions for the classical Rice-Ramsperger-Kassel-Marcus (RRKM) (i.e., RRK) and classical transition-state theory (TST) rate constants become equivalent. Using this relationship, a molecule's unimolecular rate constants versus temperature may be determined from chemical dynamics simulations of microcanonical ensembles for the molecule at different total energies. The simulation identifies the molecule's unimolecular pathways and their Arrhenius parameters. In the work presented here, this approach is used to study the thermal decomposition of CH3-NH-CH═CH-CH3, an important constituent in the polymer of cross-linked epoxy resins. Direct dynamics simulations, at the MP2/6-31+G* level of theory, were used to investigate the decomposition of microcanonical ensembles for this molecule. The Arrhenius A and Ea parameters determined from the direct dynamics simulation are in very good agreement with the TST Arrhenius parameters for the MP2/6-31+G* potential energy surface. The simulation method applied here may be particularly useful for large molecules with a multitude of decomposition pathways and whose transition states may be difficult to determine and have structures that are not readily obvious.
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Dual-wavelength pump-probe microscopy analysis of melanin composition
NASA Astrophysics Data System (ADS)
Thompson, Andrew; Robles, Francisco E.; Wilson, Jesse W.; Deb, Sanghamitra; Calderbank, Robert; Warren, Warren S.
2016-11-01
Pump-probe microscopy is an emerging technique that provides detailed chemical information of absorbers with sub-micrometer spatial resolution. Recent work has shown that the pump-probe signals from melanin in human skin cancers correlate well with clinical concern, but it has been difficult to infer the molecular origins of these differences. Here we develop a mathematical framework to describe the pump-probe dynamics of melanin in human pigmented tissue samples, which treats the ensemble of individual chromophores that make up melanin as Gaussian absorbers with bandwidth related via Frenkel excitons. Thus, observed signals result from an interplay between the spectral bandwidths of the individual underlying chromophores and spectral proximity of the pump and probe wavelengths. The model is tested using a dual-wavelength pump-probe approach and a novel signal processing method based on gnomonic projections. Results show signals can be described by a single linear transition path with different rates of progress for different individual pump-probe wavelength pairs. Moreover, the combined dual-wavelength data shows a nonlinear transition that supports our mathematical framework and the excitonic model to describe the optical properties of melanin. The novel gnomonic projection analysis can also be an attractive generic tool for analyzing mixing paths in biomolecular and analytical chemistry.
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Dual-wavelength pump-probe microscopy analysis of melanin composition
Thompson, Andrew; Robles, Francisco E.; Wilson, Jesse W.; Deb, Sanghamitra; Calderbank, Robert; Warren, Warren S.
2016-01-01
Pump-probe microscopy is an emerging technique that provides detailed chemical information of absorbers with sub-micrometer spatial resolution. Recent work has shown that the pump-probe signals from melanin in human skin cancers correlate well with clinical concern, but it has been difficult to infer the molecular origins of these differences. Here we develop a mathematical framework to describe the pump-probe dynamics of melanin in human pigmented tissue samples, which treats the ensemble of individual chromophores that make up melanin as Gaussian absorbers with bandwidth related via Frenkel excitons. Thus, observed signals result from an interplay between the spectral bandwidths of the individual underlying chromophores and spectral proximity of the pump and probe wavelengths. The model is tested using a dual-wavelength pump-probe approach and a novel signal processing method based on gnomonic projections. Results show signals can be described by a single linear transition path with different rates of progress for different individual pump-probe wavelength pairs. Moreover, the combined dual-wavelength data shows a nonlinear transition that supports our mathematical framework and the excitonic model to describe the optical properties of melanin. The novel gnomonic projection analysis can also be an attractive generic tool for analyzing mixing paths in biomolecular and analytical chemistry. PMID:27833147
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Long-time Dynamics of Stochastic Wave Breaking
NASA Astrophysics Data System (ADS)
Restrepo, J. M.; Ramirez, J. M.; Deike, L.; Melville, K.
2017-12-01
A stochastic parametrization is proposed for the dynamics of wave breaking of progressive water waves. The model is shown to agree with transport estimates, derived from the Lagrangian path of fluid parcels. These trajectories are obtained numerically and are shown to agree well with theory in the non-breaking regime. Of special interest is the impact of wave breaking on transport, momentum exchanges and energy dissipation, as well as dispersion of trajectories. The proposed model, ensemble averaged to larger time scales, is compared to ensemble averages of the numerically generated parcel dynamics, and is then used to capture energy dissipation and path dispersion.
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NASA Astrophysics Data System (ADS)
Saleh, F.; Ramaswamy, V.; Georgas, N.; Blumberg, A. F.; Wang, Y.
2016-12-01
Advances in computational resources and modeling techniques are opening the path to effectively integrate existing complex models. In the context of flood prediction, recent extreme events have demonstrated the importance of integrating components of the hydrosystem to better represent the interactions amongst different physical processes and phenomena. As such, there is a pressing need to develop holistic and cross-disciplinary modeling frameworks that effectively integrate existing models and better represent the operative dynamics. This work presents a novel Hydrologic-Hydraulic-Hydrodynamic Ensemble (H3E) flood prediction framework that operationally integrates existing predictive models representing coastal (New York Harbor Observing and Prediction System, NYHOPS), hydrologic (US Army Corps of Engineers Hydrologic Modeling System, HEC-HMS) and hydraulic (2-dimensional River Analysis System, HEC-RAS) components. The state-of-the-art framework is forced with 125 ensemble meteorological inputs from numerical weather prediction models including the Global Ensemble Forecast System, the European Centre for Medium-Range Weather Forecasts (ECMWF), the Canadian Meteorological Centre (CMC), the Short Range Ensemble Forecast (SREF) and the North American Mesoscale Forecast System (NAM). The framework produces, within a 96-hour forecast horizon, on-the-fly Google Earth flood maps that provide critical information for decision makers and emergency preparedness managers. The utility of the framework was demonstrated by retrospectively forecasting an extreme flood event, hurricane Sandy in the Passaic and Hackensack watersheds (New Jersey, USA). Hurricane Sandy caused significant damage to a number of critical facilities in this area including the New Jersey Transit's main storage and maintenance facility. The results of this work demonstrate that ensemble based frameworks provide improved flood predictions and useful information about associated uncertainties, thus improving the assessment of risks as when compared to a deterministic forecast. The work offers perspectives for short-term flood forecasts, flood mitigation strategies and best management practices for climate change scenarios.
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NASA Astrophysics Data System (ADS)
Pachov, Dimitar V.
Biomolecules are dynamic in nature and visit a number of states while performing their biological function. However, understanding how they interconvert between functional substates is a challenging task. In this thesis, we employ enhanced computational strategies to reveal in atomistic resolution transition states and molecular mechanism along conformational pathways of the signaling protein Nitrogen Regulatory Protein C (NtrC) and the enzyme Adenylate Kinase (Adk). Targeted Molecular Dynamics (TMD) simulations and NMR experiments have previously found the active/inactive interconversion of NtrC is stabilized by non-native transient contacts. To find where along the conformational pathway they lie and probe the existence of multiple intermediates, a beyond 8mus-extensive mapping of the conformational landscape was performed by a multitude of straightforward MD simulations relaxed from the biased TMD pathway. A number of metastable states stabilized by local interactions was found to underline the conformational pathway of NtrC. Two spontaneous transitions of the last stage of the active-to-inactive conversion were identified and used in path sampling procedures to generate an ensemble of truly dynamic reactive pathways. The transition state ensemble (TSE) and mechanistic descriptors of this transition were revealed in atomic detail and verified by committor analysis. By analyzing how pressure affects the dynamics and function of two homologous Adk proteins - the P.Profundum Adk surviving at 700atm pressure in the deep sea, and the E. coli Adk that lives at ambient pressures - we indirectly obtained atomic information about the TSE of the large-amplitude rate-limiting conformational opening of the Adk lids. Guided by NMR experiments showing significantly decreased activation volumes of the piezophile compared to its mesophilic counterpart, TMD simulations revealed the formation of an extended hydrogen-bonded water network in the transition state of the piezophile that can explain the experimentally measured activation volume differences. The transition state of the conformational change was proposed to lie close to the closed state. Additionally, a number of descriptors were used to characterize the free energy landscape of the mesophile. It was found that the features of landscape are highly sensitive to the binding of different ligands, their protonation states and the presence of magnesium.
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The Potential Observation Network Design with Mesoscale Ensemble Sensitivities in Complex Terrain
2012-03-01
in synoptic storms , extratropical transition and developing hurricanes. Because they rely on lagged covariances from a finite-sized ensemble, they...diagnose predictors of forecast error in synoptic storms , extratropical transition and developing hurricanes. Because they rely on lagged covariances...sensitivities can be used successfully to diagnose predictors of forecast error in synoptic storms (Torn and Hakim 2008), extratropical transition (Torn and
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Measuring excess free energies of self-assembled membrane structures.
Norizoe, Yuki; Daoulas, Kostas Ch; Müller, Marcus
2010-01-01
Using computer simulation of a solvent-free, coarse-grained model for amphiphilic membranes, we study the excess free energy of hourglass-shaped connections (i.e., stalks) between two apposed bilayer membranes. In order to calculate the free energy by simulation in the canonical ensemble, we reversibly transfer two apposed bilayers into a configuration with a stalk in three steps. First, we gradually replace the intermolecular interactions by an external, ordering field. The latter is chosen such that the structure of the non-interacting system in this field closely resembles the structure of the original, interacting system in the absence of the external field. The absence of structural changes along this path suggests that it is reversible; a fact which is confirmed by expanded-ensemble simulations. Second, the external, ordering field is changed as to transform the non-interacting system from the apposed bilayer structure to two-bilayers connected by a stalk. The final external field is chosen such that the structure of the non-interacting system resembles the structure of the stalk in the interacting system without a field. On the third branch of the transformation path, we reversibly replace the external, ordering field by non-bonded interactions. Using expanded-ensemble techniques, the free energy change along this reversible path can be obtained with an accuracy of 10(-3)k(B)T per molecule in the n VT-ensemble. Calculating the chemical potential, we obtain the free energy of a stalk in the grandcanonical ensemble, and employing semi-grandcanonical techniques, we calculate the change of the excess free energy upon altering the molecular architecture. This computational strategy can be applied to compute the free energy of self-assembled phases in lipid and copolymer systems, and the excess free energy of defects or interfaces.
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Reaction mechanism and reaction coordinates from the viewpoint of energy flow
2016-01-01
Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition. PMID:27004858
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Reaction mechanism and reaction coordinates from the viewpoint of energy flow
DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, Wenjin; Ma, Ao, E-mail: aoma@uic.edu
Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C{sub 7eq} → C{sub 7ax} transition of themore » alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.« less
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A stochastic Markov chain model to describe lung cancer growth and metastasis.
Newton, Paul K; Mason, Jeremy; Bethel, Kelly; Bazhenova, Lyudmila A; Nieva, Jorge; Kuhn, Peter
2012-01-01
A stochastic Markov chain model for metastatic progression is developed for primary lung cancer based on a network construction of metastatic sites with dynamics modeled as an ensemble of random walkers on the network. We calculate a transition matrix, with entries (transition probabilities) interpreted as random variables, and use it to construct a circular bi-directional network of primary and metastatic locations based on postmortem tissue analysis of 3827 autopsies on untreated patients documenting all primary tumor locations and metastatic sites from this population. The resulting 50 potential metastatic sites are connected by directed edges with distributed weightings, where the site connections and weightings are obtained by calculating the entries of an ensemble of transition matrices so that the steady-state distribution obtained from the long-time limit of the Markov chain dynamical system corresponds to the ensemble metastatic distribution obtained from the autopsy data set. We condition our search for a transition matrix on an initial distribution of metastatic tumors obtained from the data set. Through an iterative numerical search procedure, we adjust the entries of a sequence of approximations until a transition matrix with the correct steady-state is found (up to a numerical threshold). Since this constrained linear optimization problem is underdetermined, we characterize the statistical variance of the ensemble of transition matrices calculated using the means and variances of their singular value distributions as a diagnostic tool. We interpret the ensemble averaged transition probabilities as (approximately) normally distributed random variables. The model allows us to simulate and quantify disease progression pathways and timescales of progression from the lung position to other sites and we highlight several key findings based on the model.
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Skvortsov, Alexander M; Klushin, Leonid I; Polotsky, Alexey A; Binder, Kurt
2012-03-01
The phase transition occurring when a single polymer chain adsorbed at a planar solid surface is mechanically desorbed is analyzed in two statistical ensembles. In the force ensemble, a constant force applied to the nongrafted end of the chain (that is grafted at its other end) is used as a given external control variable. In the z-ensemble, the displacement z of this nongrafted end from the surface is taken as the externally controlled variable. Basic thermodynamic parameters, such as the adsorption energy, exhibit a very different behavior as a function of these control parameters. In the thermodynamic limit of infinite chain length the desorption transition with the force as a control parameter clearly is discontinuous, while in the z-ensemble continuous variations are found. However, one should not be misled by a too-naive application of the Ehrenfest criterion to consider the transition as a continuous transition: rather, one traverses a two-phase coexistence region, where part of the chain is still adsorbed and the other part desorbed and stretched. Similarities with and differences from two-phase coexistence at vapor-liquid transitions are pointed out. The rounding of the singularities due to finite chain length is illustrated by exact calculations for the nonreversal random walk model on the simple cubic lattice. A new concept of local order parameter profiles for the description of the mechanical desorption of adsorbed polymers is suggested. This concept give evidence for both the existence of two-phase coexistence within single polymer chains for this transition and the anomalous character of this two-phase coexistence. Consequences for the proper interpretation of experiments performed in different ensembles are briefly mentioned.
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Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark
2018-04-10
Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of reaction rates and an improved understanding of activated states.
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Instanton-dyon ensembles reproduce deconfinement and chiral restoration phase transitions
NASA Astrophysics Data System (ADS)
Shuryak, Edward
2018-03-01
Paradigm shift in gauge topology at finite temperatures, from the instantons to their constituents - instanton-dyons - has recently lead to studies of their ensembles and very significant advances. Like instantons, they have fermionic zero modes, and their collectivization at suffciently high density explains the chiral symmetry breaking transition. Unlike instantons, these objects have electric and magnetic charges. Simulations of the instanton-dyon ensembles have demonstrated that their back reaction on the Polyakov line modifies its potential and generates the deconfinement phase transition. For the Nc = 2 gauge theory the transition is second order, for QCD-like theory with Nc = 2 and two light quark flavors Nf = 2 both transitions are weak crossovers at happening at about the same condition. Introduction of quark-flavor-dependent periodicity phases (imaginary chemical potentials) leads to drastic changes in both transitions. In particulaly, in the so called Z(Nc) - QCD model the deconfinement transforms to strong first order transition, while the chiral condensate does not disappear at all. The talk will also cover more detailed studies of correlations between the dyons, effective eta' mass and other screening masses.
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Transition path time distributions
NASA Astrophysics Data System (ADS)
Laleman, M.; Carlon, E.; Orland, H.
2017-12-01
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the barrier. Average transition path times and, recently, their full probability distribution have been measured for several biomolecular systems, e.g., in the folding of nucleic acids or proteins. Motivated by these experiments, we have calculated the full transition path time distribution for a single stochastic particle crossing a parabolic barrier, including inertial terms which were neglected in previous studies. These terms influence the short time scale dynamics of a stochastic system and can be of experimental relevance in view of the short duration of transition paths. We derive the full transition path time distribution as well as the average transition path times and discuss the similarities and differences with the high friction limit.
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Transition-Metal Chalcogenide/Graphene Ensembles for Light-Induced Energy Applications.
Kagkoura, Antonia; Skaltsas, Theodosis; Tagmatarchis, Nikos
2017-09-21
Recently, nanomaterials that harvest solar energy and convert it to other forms of energy are of great interest. In this context, transition metal chalcogenides (TMCs) have recently been in the spotlight due to their optoelectronic properties that render them potential candidates mainly in energy conversion applications. Integration of TMCs onto a strong electron-accepting material, such as graphene, yielding novel TMC/graphene ensembles is of high significance, since photoinduced charge-transfer phenomena, leading to intra-ensemble charge separation, may occur. In this review, we highlight the utility of TMC/graphene ensembles, with a specific focus on latest trends in applications, while their synthetic routes are also discussed. In fact, TMC/graphene ensembles are photocatalytically active and superior as compared to intact TMCs analogues, when examined toward photocatalytic H 2 evolution, dye degradation and redox transformations of organic compounds. Moreover, TMC/graphene ensembles have shown excellent prospect when employed in photovoltaics and biosensing applications. Finally, the future prospects of such materials are outlined. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Progress Toward an Neutral Yb Frequency Standard
NASA Astrophysics Data System (ADS)
Cramer, Claire; Hong, Tao; Nagourney, Warren; Fortson, Norval
2004-05-01
We report recent progress toward a direct observation of the ^1S_0^ -- ^3P0 clock transition at 578 nm in atomic Yb and review the experimental path to an optical frequency standard based on neutral Yb confined in a Stark-free optical lattice. Lamb-Dicke confinement in an optical lattice at the ``magic wavelength'' (λ _M) at which ground and excited state light shifts cancel will free the spectrum from Doppler and recoil shifts, providing an optimal environment for a clock consisting of an ensemble of cold, trapped atoms. In^171Yb the ^3P0 level has a hfs induced lifetime of 21 s. With this isotope in a Stark-free lattice at λ M ng 750 nm, perturbations to the clock energy levels can be held below the mHz level, providing an accuracy of a few parts in 10^18[1]. To observe the clock transition we use a shelving scheme that creates a leak in a MOT on the ^1S_0^ -- ^1P1 transition. A laser resonant with the clock transition drives atoms into the ^3P0 state, in which they can escape the MOT, leading to an observable decrease in MOT fluorescence. [1] S. Porsev and A. Derevianko, to be published in PRA
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Entanglement between two spatially separated atomic modes
NASA Astrophysics Data System (ADS)
Lange, Karsten; Peise, Jan; Lücke, Bernd; Kruse, Ilka; Vitagliano, Giuseppe; Apellaniz, Iagoba; Kleinmann, Matthias; Tóth, Géza; Klempt, Carsten
2018-04-01
Modern quantum technologies in the fields of quantum computing, quantum simulation, and quantum metrology require the creation and control of large ensembles of entangled particles. In ultracold ensembles of neutral atoms, nonclassical states have been generated with mutual entanglement among thousands of particles. The entanglement generation relies on the fundamental particle-exchange symmetry in ensembles of identical particles, which lacks the standard notion of entanglement between clearly definable subsystems. Here, we present the generation of entanglement between two spatially separated clouds by splitting an ensemble of ultracold identical particles prepared in a twin Fock state. Because the clouds can be addressed individually, our experiments open a path to exploit the available entangled states of indistinguishable particles for quantum information applications.
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Fast and slow transitions in frontal ensemble activity during flexible sensorimotor behavior.
Siniscalchi, Michael J; Phoumthipphavong, Victoria; Ali, Farhan; Lozano, Marc; Kwan, Alex C
2016-09-01
The ability to shift between repetitive and goal-directed actions is a hallmark of cognitive control. Previous studies have reported that adaptive shifts in behavior are accompanied by changes of neural activity in frontal cortex. However, neural and behavioral adaptations can occur at multiple time scales, and their relationship remains poorly defined. Here we developed an adaptive sensorimotor decision-making task for head-fixed mice, requiring them to shift flexibly between multiple auditory-motor mappings. Two-photon calcium imaging of secondary motor cortex (M2) revealed different ensemble activity states for each mapping. When adapting to a conditional mapping, transitions in ensemble activity were abrupt and occurred before the recovery of behavioral performance. By contrast, gradual and delayed transitions accompanied shifts toward repetitive responding. These results demonstrate distinct ensemble signatures associated with the start versus end of sensory-guided behavior and suggest that M2 leads in engaging goal-directed response strategies that require sensorimotor associations.
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Transition path time distributions for Lévy flights
NASA Astrophysics Data System (ADS)
Janakiraman, Deepika
2018-07-01
This paper presents a study of transition path time distributions for Lévy noise-induced barrier crossing. Transition paths are short segments of the reactive trajectories and span the barrier region of the potential without spilling into the reactant/product wells. The time taken to traverse this segment is referred to as the transition path time. Since the transition path is devoid of excursions in the minimum, the corresponding time will give the exclusive barrier crossing time, unlike . This work explores the distribution of transition path times for superdiffusive barrier crossing, analytically. This is made possible by approximating the barrier by an inverted parabola. Using this approximation, the distributions are evaluated in both over- and under-damped limits of friction. The short-time behaviour of the distributions, provide analytical evidence for single-step transition events—a feature in Lévy-barrier crossing as observed in prior simulation studies. The average transition path time is calculated as a function of the Lévy index (α), and the optimal value of α leading to minimum average transition path time is discussed, in both the limits of friction. Langevin dynamics simulations corroborating with the analytical results are also presented.
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Transition path time distribution and the transition path free energy barrier.
Pollak, Eli
2016-10-19
The recent experimental measurement of the transition path time distributions of proteins presents several challenges to theory. Firstly, why do the fits of the experimental data to a theoretical expression lead to barrier heights which are much lower than the free energies of activation of the observed transitions? Secondly, there is the theoretical question of determining the transition path time distribution, without invoking the Smoluchowski limit. In this paper, we derive an exact expression for a transition path time distribution which is valid for arbitrary memory friction using the normal mode transformation which underlies Kramers' rate theory. We then recall that for low barriers, there is a noticeable difference between the transition path time distribution obtained with absorbing boundary conditions and free boundary conditions. For the former, the transition times are shorter, since recrossings of the boundaries are disallowed. As a result, if one uses the distribution based on absorbing boundary conditions to fit the experimental data, one will find that the transition path barrier will be larger than the values found based on a theory with free boundary conditions. We then introduce the paradigm of a transition path barrier height, and show that one should always expect it to be much smaller than the activation energy.
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NASA Astrophysics Data System (ADS)
Rybalova, Elena; Semenova, Nadezhda; Strelkova, Galina; Anishchenko, Vadim
2017-06-01
We study the transition from coherence (complete synchronization) to incoherence (spatio-temporal chaos) in ensembles of nonlocally coupled chaotic maps with nonhyperbolic and hyperbolic attractors. As basic models of a partial element we use the Henon map and the Lozi map. We show that the transition to incoherence in a ring of coupled Henon maps occurs through the appearance of phase and amplitude chimera states. An ensemble of coupled Lozi maps demonstrates the coherence-incoherence transition via solitary states and no chimera states are observed in this case.
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NASA Astrophysics Data System (ADS)
Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui
2016-04-01
Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao; Huang, Xuhui, E-mail: xuhuihuang@ust.hk
2016-04-21
Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kineticsmore » are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.« less
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Kukic, Predrag; Lundström, Patrik; Camilloni, Carlo; Evenäs, Johan; Akke, Mikael; Vendruscolo, Michele
2016-01-12
Calmodulin is a two-domain signaling protein that becomes activated upon binding cooperatively two pairs of calcium ions, leading to large-scale conformational changes that expose its binding site. Despite significant advances in understanding the structural biology of calmodulin functions, the mechanistic details of the conformational transition between closed and open states have remained unclear. To investigate this transition, we used a combination of molecular dynamics simulations and nuclear magnetic resonance (NMR) experiments on the Ca(2+)-saturated E140Q C-terminal domain variant. Using chemical shift restraints in replica-averaged metadynamics simulations, we obtained a high-resolution structural ensemble consisting of two conformational states and validated such an ensemble against three independent experimental data sets, namely, interproton nuclear Overhauser enhancements, (15)N order parameters, and chemical shift differences between the exchanging states. Through a detailed analysis of this structural ensemble and of the corresponding statistical weights, we characterized a calcium-mediated conformational transition whereby the coordination of Ca(2+) by just one oxygen of the bidentate ligand E140 triggers a concerted movement of the two EF-hands that exposes the target binding site. This analysis provides atomistic insights into a possible Ca(2+)-mediated activation mechanism of calmodulin that cannot be achieved from static structures alone or from ensemble NMR measurements of the transition between conformations.
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Chandrasekaran, Srinivas Niranj; Das, Jhuma; Dokholyan, Nikolay V.; Carter, Charles W.
2016-01-01
PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. PMID:26958584
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NASA Astrophysics Data System (ADS)
Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.
2001-03-01
Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.
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Generalized ensemble method applied to study systems with strong first order transitions
Malolepsza, E.; Kim, J.; Keyes, T.
2015-09-28
At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub, where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM).more » This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. Lastly, the method is illustrated in a study of the very strong solid/liquid transition in water.« less
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Chimera at the phase-flip transition of an ensemble of identical nonlinear oscillators
NASA Astrophysics Data System (ADS)
Gopal, R.; Chandrasekar, V. K.; Senthilkumar, D. V.; Venkatesan, A.; Lakshmanan, M.
2018-06-01
A complex collective emerging behavior characterized by coexisting coherent and incoherent domains is termed as a chimera state. We bring out the existence of a new type of chimera in a nonlocally coupled ensemble of identical oscillators driven by a common dynamic environment. The latter facilitates the onset of phase-flip bifurcation/transitions among the coupled oscillators of the ensemble, while the nonlocal coupling induces a partial asynchronization among the out-of-phase synchronized oscillators at this onset. This leads to the manifestation of coexisting out-of-phase synchronized coherent domains interspersed by asynchronous incoherent domains elucidating the existence of a different type of chimera state. In addition to this, a rich variety of other collective behaviors such as clusters with phase-flip transition, conventional chimera, solitary state and complete synchronized state which have been reported using different coupling architectures are found to be induced by the employed couplings for appropriate coupling strengths. The robustness of the resulting dynamics is demonstrated in ensembles of two paradigmatic models, namely Rössler oscillators and Stuart-Landau oscillators.
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Generalized ensemble method applied to study systems with strong first order transitions
NASA Astrophysics Data System (ADS)
Małolepsza, E.; Kim, J.; Keyes, T.
2015-09-01
At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub [1], where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM). This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. The method is illustrated in a study of the very strong solid/liquid transition in water.
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NASA Astrophysics Data System (ADS)
Sherkatghanad, Zeinab; Mirza, Behrouz; Mirzaiyan, Zahra; Mansoori, Seyed Ali Hosseini
We consider the critical behaviors and phase transitions of Gauss-Bonnet-Born-Infeld-AdS black holes (GB-BI-AdS) for d = 5, 6 and the extended phase space. We assume the cosmological constant, Λ, the coupling coefficient α, and the BI parameter β to be thermodynamic pressures of the system. Having made these assumptions, the critical behaviors are then studied in the two canonical and grand canonical ensembles. We find “reentrant and triple point phase transitions” (RPT-TP) and “multiple reentrant phase transitions” (multiple RPT) with increasing pressure of the system for specific values of the coupling coefficient α in the canonical ensemble. Also, we observe a reentrant phase transition (RPT) of GB-BI-AdS black holes in the grand canonical ensemble and for d = 6. These calculations are then expanded to the critical behavior of Born-Infeld-AdS (BI-AdS) black holes in the third-order of Lovelock gravity and in the grand canonical ensemble to find a van der Waals (vdW) behavior for d = 7 and a RPT for d = 8 for specific values of potential ϕ in the grand canonical ensemble. Furthermore, we obtain a similar behavior for the limit of β →∞, i.e. charged-AdS black holes in the third-order of the Lovelock gravity. Thus, it is shown that the critical behaviors of these black holes are independent of the parameter β in the grand canonical ensemble.
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Fluctuating observation time ensembles in the thermodynamics of trajectories
NASA Astrophysics Data System (ADS)
Budini, Adrián A.; Turner, Robert M.; Garrahan, Juan P.
2014-03-01
The dynamics of stochastic systems, both classical and quantum, can be studied by analysing the statistical properties of dynamical trajectories. The properties of ensembles of such trajectories for long, but fixed, times are described by large-deviation (LD) rate functions. These LD functions play the role of dynamical free energies: they are cumulant generating functions for time-integrated observables, and their analytic structure encodes dynamical phase behaviour. This ‘thermodynamics of trajectories’ approach is to trajectories and dynamics what the equilibrium ensemble method of statistical mechanics is to configurations and statics. Here we show that, just like in the static case, there are a variety of alternative ensembles of trajectories, each defined by their global constraints, with that of trajectories of fixed total time being just one of these. We show how the LD functions that describe an ensemble of trajectories where some time-extensive quantity is constant (and large) but where total observation time fluctuates can be mapped to those of the fixed-time ensemble. We discuss how the correspondence between generalized ensembles can be exploited in path sampling schemes for generating rare dynamical trajectories.
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Kinetics and reaction coordinates of the reassembly of protein fragments via forward flux sampling.
Borrero, Ernesto E; Contreras Martínez, Lydia M; DeLisa, Matthew P; Escobedo, Fernando A
2010-05-19
We studied the mechanism of the reassembly and folding process of two fragments of a split lattice protein by using forward flux sampling (FFS). Our results confirmed previous thermodynamics and kinetics analyses that suggested that the disruption of the critical core (of an unsplit protein that folds by a nucleation mechanism) plays a key role in the reassembly mechanism of the split system. For several split systems derived from a parent 48-mer model, we estimated the reaction coordinates in terms of collective variables by using the FFS least-square estimation method and found that the reassembly transition is best described by a combination of the total number of native contacts, the number of interchain native contacts, and the total conformational energy of the split system. We also analyzed the transition path ensemble obtained from FFS simulations using the estimated reaction coordinates as order parameters to identify the microscopic features that differentiate the reassembly of the different split systems studied. We found that in the fastest folding split system, a balanced distribution of the original-core amino acids (of the unsplit system) between protein fragments propitiates interchain interactions at early stages of the folding process. Only this system exhibits a different reassembly mechanism from that of the unsplit protein, involving the formation of a different folding nucleus. In the slowest folding system, the concentration of the folding nucleus in one fragment causes its early prefolding, whereas the second fragment tends to remain as a detached random coil. We also show that the reassembly rate can be either increased or decreased by tuning interchain cooperativeness via the introduction of a single point mutation that either strengthens or weakens one of the native interchain contacts (prevalent in the transition state ensemble). Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Method and apparatus for quantum information processing using entangled neutral-atom qubits
Jau, Yuan Yu; Biedermann, Grant; Deutsch, Ivan
2018-04-03
A method for preparing an entangled quantum state of an atomic ensemble is provided. The method includes loading each atom of the atomic ensemble into a respective optical trap; placing each atom of the atomic ensemble into a same first atomic quantum state by impingement of pump radiation; approaching the atoms of the atomic ensemble to within a dipole-dipole interaction length of each other; Rydberg-dressing the atomic ensemble; during the Rydberg-dressing operation, exciting the atomic ensemble with a Raman pulse tuned to stimulate a ground-state hyperfine transition from the first atomic quantum state to a second atomic quantum state; and separating the atoms of the atomic ensemble by more than a dipole-dipole interaction length.
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Parameter optimization on the convergence surface of path simulations
NASA Astrophysics Data System (ADS)
Chandrasekaran, Srinivas Niranj
Computational treatments of protein conformational changes tend to focus on the trajectories themselves, despite the fact that it is the transition state structures that contain information about the barriers that impose multi-state behavior. PATH is an algorithm that computes a transition pathway between two protein crystal structures, along with the transition state structure, by minimizing the Onsager-Machlup action functional. It is rapid but depends on several unknown input parameters whose range of different values can potentially generate different transition-state structures. Transition-state structures arising from different input parameters cannot be uniquely compared with those generated by other methods. I outline modifications that I have made to the PATH algorithm that estimates these input parameters in a manner that circumvents these difficulties, and describe two complementary tests that validate the transition-state structures found by the PATH algorithm. First, I show that although the PATH algorithm and two other approaches to computing transition pathways produce different low-energy structures connecting the initial and final ground-states with the transition state, all three methods agree closely on the configurations of their transition states. Second, I show that the PATH transition states are close to the saddle points of free-energy surfaces connecting initial and final states generated by replica-exchange Discrete Molecular Dynamics simulations. I show that aromatic side-chain rearrangements create similar potential energy barriers in the transition-state structures identified by PATH for a signaling protein, a contractile protein, and an enzyme. Finally, I observed, but cannot account for, the fact that trajectories obtained for all-atom and Calpha-only simulations identify transition state structures in which the Calpha atoms are in essentially the same positions. The consistency between transition-state structures derived by different algorithms for unrelated protein systems argues that although functionally important protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. In the end, I outline the strategies that could enhance the efficiency and applicability of PATH.
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The Ensemble Space Weather Modeling System (eSWMS): Status, Capabilities and Challenges
NASA Astrophysics Data System (ADS)
Fry, C. D.; Eccles, J. V.; Reich, J. P.
2010-12-01
Marking a milestone in space weather forecasting, the Space Weather Modeling System (SWMS) successfully completed validation testing in advance of operational testing at Air Force Weather Agency’s primary space weather production center. This is the first coupling of stand-alone, physics-based space weather models that are currently in operations at AFWA supporting the warfighter. Significant development effort went into ensuring the component models were portable and scalable while maintaining consistent results across diverse high performance computing platforms. Coupling was accomplished under the Earth System Modeling Framework (ESMF). The coupled space weather models are the Hakamada-Akasofu-Fry version 2 (HAFv2) solar wind model and GAIM1, the ionospheric forecast component of the Global Assimilation of Ionospheric Measurements (GAIM) model. The SWMS was developed by team members from AFWA, Explorations Physics International, Inc. (EXPI) and Space Environment Corporation (SEC). The successful development of the SWMS provides new capabilities beyond enabling extended lead-time, data-driven ionospheric forecasts. These include ingesting diverse data sets at higher resolution, incorporating denser computational grids at finer time steps, and performing probability-based ensemble forecasts. Work of the SWMS development team now focuses on implementing the ensemble-based probability forecast capability by feeding multiple scenarios of 5 days of solar wind forecasts to the GAIM1 model based on the variation of the input fields to the HAFv2 model. The ensemble SWMS (eSWMS) will provide the most-likely space weather scenario with uncertainty estimates for important forecast fields. The eSWMS will allow DoD mission planners to consider the effects of space weather on their systems with more advance warning than is currently possible. The payoff is enhanced, tailored support to the warfighter with improved capabilities, such as point-to-point HF propagation forecasts, single-frequency GPS error corrections, and high cadence, high-resolution Space Situational Awareness (SSA) products. We present the current status of eSWMS, its capabilities, limitations and path of transition to operational use.
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Transition-State Ensembles Navigate the Pathways of Enzyme Catalysis.
Mickert, Matthias J; Gorris, Hans H
2018-06-07
Transition-state theory (TST) provides an important framework for analyzing and explaining the reaction rates of enzymes. TST, however, needs to account for protein dynamic effects and heterogeneities in enzyme catalysis. We have analyzed the reaction rates of β-galactosidase and β-glucuronidase at the single molecule level by using large arrays of femtoliter-sized chambers. Heterogeneities in individual reaction rates yield information on the intrinsic distribution of the free energy of activation (Δ G ‡ ) in an enzyme ensemble. The broader distribution of Δ G ‡ in β-galactosidase compared to β-glucuronidase is attributed to β-galactosidase's multiple catalytic functions as a hydrolase and a transglycosylase. Based on the catalytic mechanism of β-galactosidase, we show that transition-state ensembles do not only contribute to enzyme catalysis but can also channel the catalytic pathway to the formation of different products. We conclude that β-galactosidase is an example of natural evolution, where a new catalytic pathway branches off from an established enzyme function. The functional division of work between enzymatic substates explains why the conformational space represented by the enzyme ensemble is larger than the conformational space that can be sampled by any given enzyme molecule during catalysis.
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PhytoPath: an integrative resource for plant pathogen genomics.
Pedro, Helder; Maheswari, Uma; Urban, Martin; Irvine, Alistair George; Cuzick, Alayne; McDowall, Mark D; Staines, Daniel M; Kulesha, Eugene; Hammond-Kosack, Kim Elizabeth; Kersey, Paul Julian
2016-01-04
PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways
Fried, Jake Y.; Luna, Augustin
2013-01-01
Purpose: The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries. Availability: The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License. Contact: augustin@mail.nih.gov or jakeyfried@gmail.com PMID:23547033
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NASA Astrophysics Data System (ADS)
Bouchet, Freddy; Laurie, Jason; Zaboronski, Oleg
2014-09-01
We investigate a class of simple models for Langevin dynamics of turbulent flows, including the one-layer quasi-geostrophic equation and the two-dimensional Euler equations. Starting from a path integral representation of the transition probability, we compute the most probable fluctuation paths from one attractor to any state within its basin of attraction. We prove that such fluctuation paths are the time reversed trajectories of the relaxation paths for a corresponding dual dynamics, which are also within the framework of quasi-geostrophic Langevin dynamics. Cases with or without detailed balance are studied. We discuss a specific example for which the stationary measure displays either a second order (continuous) or a first order (discontinuous) phase transition and a tricritical point. In situations where a first order phase transition is observed, the dynamics are bistable. Then, the transition paths between two coexisting attractors are instantons (fluctuation paths from an attractor to a saddle), which are related to the relaxation paths of the corresponding dual dynamics. For this example, we show how one can analytically determine the instantons and compute the transition probabilities for rare transitions between two attractors.
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NASA Astrophysics Data System (ADS)
Hoteit, I.; Hollt, T.; Hadwiger, M.; Knio, O. M.; Gopalakrishnan, G.; Zhan, P.
2016-02-01
Ocean reanalyses and forecasts are nowadays generated by combining ensemble simulations with data assimilation techniques. Most of these techniques resample the ensemble members after each assimilation cycle. Tracking behavior over time, such as all possible paths of a particle in an ensemble vector field, becomes very difficult, as the number of combinations rises exponentially with the number of assimilation cycles. In general a single possible path is not of interest but only the probabilities that any point in space might be reached by a particle at some point in time. We present an approach using probability-weighted piecewise particle trajectories to allow for interactive probability mapping. This is achieved by binning the domain and splitting up the tracing process into the individual assimilation cycles, so that particles that fall into the same bin after a cycle can be treated as a single particle with a larger probability as input for the next cycle. As a result we loose the possibility to track individual particles, but can create probability maps for any desired seed at interactive rates. The technique is integrated in an interactive visualization system that enables the visual analysis of the particle traces side by side with other forecast variables, such as the sea surface height, and their corresponding behavior over time. By harnessing the power of modern graphics processing units (GPUs) for visualization as well as computation, our system allows the user to browse through the simulation ensembles in real-time, view specific parameter settings or simulation models and move between different spatial or temporal regions without delay. In addition our system provides advanced visualizations to highlight the uncertainty, or show the complete distribution of the simulations at user-defined positions over the complete time series of the domain.
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Resonance fluorescence trajectories in superconducting qubit
NASA Astrophysics Data System (ADS)
Naghiloo, Mahdi; Tan, Dian; Harrington, Patrick; Lewalle, Philippe; Jordan, Andrew; Murch, Kater
We employ phase-sensitive amplification to perform homodyne detection of the resonance fluorescence from a driven superconducting artificial atom. Entanglement between the emitter and its fluorescence allows us to track the individual quantum state trajectories of the emitter. We analyze the ensemble properties of these trajectories by considering paths that connect specific initial and final states. By applying a stochastic path integral formalism, we calculate equations of motion for the most likely path between two quantum states and compare these predicted paths to experimental data. Drawing on the mathematical similarity between the action formalism of the most likely quantum paths and ray optics, we study the emergence of caustics in quantum trajectories-situations where multiple extrema in the stochastic action occur. We observe such multiple most likely paths in experimental data and find these paths to be in reasonable quantitative agreement with theoretical calculations. Supported by the John Templeton Foundation.
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Assessment of Crack Path Prediction in Non-Proportional Mixed-Mode Fatigue
NASA Technical Reports Server (NTRS)
Highsmith, Shelby, Jr.; Johnson, Steve; Swanson, Gregory; Sayyah, Tarek; Pettit, Richard
2008-01-01
Non-proportional mixed-mode loading is present in many systems and a growing crack can experience any manner of mixed-mode loading. Prediction of the resulting crack path is important when assessing potential failure modes or when performing a failure investigation. Current crack path selection criteria are presented along with data for Inconel 718 under non-proportional mixed-mode loading. Mixed-mode crack growth can transition between path deflection mechanisms with very different orientations. Non-proportional fatigue loadings lack a single parameter for input to current crack path criteria. Crack growth transitions were observed in proportional and non-proportional FCG tests. Different paths displayed distinct fracture surface morphologies. New crack path drivers & transition criteria must be developed.
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Breaking Quantum and Thermal Limits on Precision Measurements
NASA Astrophysics Data System (ADS)
Thompson, James K.
2016-05-01
I will give an overview of our efforts to use correlations and entanglement between many atoms to overcome quantum and thermal limits on precision measurements. In the first portion of my talk, I will present a path toward a 10000 times reduced sensitivity to the thermal mirror motion that limits the linewidth of today's best lasers. By utilizing narrow atomic transitions, the laser's phase information is primarily stored in the atomic gain medium rather than in the vibration-sensitive cavity field. To this end, I will present the first observation of lasing based on the mHz linewidth optical-clock transition in a laser-cooled ensemble of strontium atoms. In the second portion of my talk, I will describe how we use collective measurements to surpass the standard quantum limit on phase estimation 1 /√{ N} for N unentangled atoms. We achieve a directly observed reduction in phase variance relative to the standard quantum limit of as much as 17.7(6) dB. Supported by DARPA QuASAR, NIST, ARO, and NSF PFC. This material is based upon work supported by the National Science Foundation under Grant Number 1125844 Physics Frontier Center.
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Baxa, Michael C.; Yu, Wookyung; Adhikari, Aashish N.; Ge, Liang; Xia, Zhen; Zhou, Ruhong; Freed, Karl F.; Sosnick, Tobin R.
2015-01-01
Experimental and computational folding studies of Proteins L & G and NuG2 typically find that sequence differences determine which of the two hairpins is formed in the transition state ensemble (TSE). However, our recent work on Protein L finds that its TSE contains both hairpins, compelling a reassessment of the influence of sequence on the folding behavior of the other two homologs. We characterize the TSEs for Protein G and NuG2b, a triple mutant of NuG2, using ψ analysis, a method for identifying contacts in the TSE. All three homologs are found to share a common and near-native TSE topology with interactions between all four strands. However, the helical content varies in the TSE, being largely absent in Proteins G & L but partially present in NuG2b. The variability likely arises from competing propensities for the formation of nonnative β turns in the naturally occurring proteins, as observed in our TerItFix folding algorithm. All-atom folding simulations of NuG2b recapitulate the observed TSEs with four strands for 5 of 27 transition paths [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. Our data support the view that homologous proteins have similar folding mechanisms, even when nonnative interactions are present in the transition state. These findings emphasize the ongoing challenge of accurately characterizing and predicting TSEs, even for relatively simple proteins. PMID:26100906
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Transitioning to a narrow path: the impact of fear of falling in older adults.
Dunlap, Pamela; Perera, Subashan; VanSwearingen, Jessie M; Wert, David; Brach, Jennifer S
2012-01-01
Everyday ambulation requires navigation of variable terrain, transitions from wide to narrow pathways, and avoiding obstacles. While the effect of age on the transition to a narrow path has been examined briefly, little is known about the impact of fear of falling on gait during the transition to a narrow path. The purpose was to examine the effect of age and fear of falling on gait during transition to a narrow path. In 31 young, mean age=25.3 years, and 30 older adults, mean age=79.6 years, step length, step time, step width and gait speed were examined during usual and transition to narrow pathway using an instrumented walkway. During the transition to narrow walk condition, fearful older adults compared to young had a wider step width (0.06 m vs 0.04 m) prior to the narrow path and took shorter steps (0.53 m vs 0.72 m; p<0.001). Compared to non-fearful older adults, fearful older adults walked slower and took shorter steps during narrow path walking (gait speed: 1.1m/s vs 0.82 m/s; p=0.01; step length: 0.60 m vs 0.47 m; p=0.03). In young and non-fearful older adults narrow path gait was similar to usual gait. Whereas older adults who were fearful, walked slower (0.82 m/s vs 0.91 m/s; p=0.001) and took shorter steps (0.44 m vs 0.53 m; p=0.004) during narrow path walking compared to usual walking. Changes in gait characteristics with transitioning to a narrow pathway were greater for fear of falling than for age. Copyright © 2011 Elsevier B.V. All rights reserved.
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Complete analysis of ensemble inequivalence in the Blume-Emery-Griffiths model
NASA Astrophysics Data System (ADS)
Hovhannisyan, V. V.; Ananikian, N. S.; Campa, A.; Ruffo, S.
2017-12-01
We study inequivalence of canonical and microcanonical ensembles in the mean-field Blume-Emery-Griffiths model. This generalizes previous results obtained for the Blume-Capel model. The phase diagram strongly depends on the value of the biquadratic exchange interaction K , the additional feature present in the Blume-Emery-Griffiths model. At small values of K , as for the Blume-Capel model, lines of first- and second-order phase transitions between a ferromagnetic and a paramagnetic phase are present, separated by a tricritical point whose location is different in the two ensembles. At higher values of K the phase diagram changes substantially, with the appearance of a triple point in the canonical ensemble, which does not find any correspondence in the microcanonical ensemble. Moreover, one of the first-order lines that starts from the triple point ends in a critical point, whose position in the phase diagram is different in the two ensembles. This line separates two paramagnetic phases characterized by a different value of the quadrupole moment. These features were not previously studied for other models and substantially enrich the landscape of ensemble inequivalence, identifying new aspects that had been discussed in a classification of phase transitions based on singularity theory. Finally, we discuss ergodicity breaking, which is highlighted by the presence of gaps in the accessible values of magnetization at low energies: it also displays new interesting patterns that are not present in the Blume-Capel model.
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Stability and Noise-induced Transitions in an Ensemble of Nonlocally Coupled Chaotic Maps
NASA Astrophysics Data System (ADS)
Bukh, Andrei V.; Slepnev, Andrei V.; Anishchenko, Vadim S.; Vadivasova, Tatiana E.
2018-05-01
The influence of noise on chimera states arising in ensembles of nonlocally coupled chaotic maps is studied. There are two types of chimera structures that can be obtained in such ensembles: phase and amplitude chimera states. In this work, a series of numerical experiments is carried out to uncover the impact of noise on both types of chimeras. The noise influence on a chimera state in the regime of periodic dynamics results in the transition to chaotic dynamics. At the same time, the transformation of incoherence clusters of the phase chimera to incoherence clusters of the amplitude chimera occurs. Moreover, it is established that the noise impact may result in the appearance of a cluster with incoherent behavior in the middle of a coherence cluster.
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Quantifying new water fractions and water age distributions using ensemble hydrograph separation
NASA Astrophysics Data System (ADS)
Kirchner, James
2017-04-01
Catchment transit times are important controls on contaminant transport, weathering rates, and runoff chemistry. Recent theoretical studies have shown that catchment transit time distributions are nonstationary, reflecting the temporal variability in precipitation forcing, the structural heterogeneity of catchments themselves, and the nonlinearity of the mechanisms controlling storage and transport in the subsurface. The challenge of empirically estimating these nonstationary transit time distributions in real-world catchments, however, has only begun to be explored. Long, high-frequency tracer time series are now becoming available, creating new opportunities to study how rainfall becomes streamflow on timescales of minutes to days following the onset of precipitation. Here I show that the conventional formula used for hydrograph separation can be converted into an equivalent linear regression equation that quantifies the fraction of current rainfall in streamflow across ensembles of precipitation events. These ensembles can be selected to represent different discharge ranges, different precipitation intensities, or different levels of antecedent moisture, thus quantifying how the fraction of "new water" in streamflow varies with forcings such as these. I further show how this approach can be generalized to empirically determine the contributions of precipitation inputs to streamflow across a range of time lags. In this way the short-term tail of the transit time distribution can be directly quantified for an ensemble of precipitation events. Benchmark testing with a simple, nonlinear, nonstationary catchment model demonstrates that this approach quantitatively measures the short tail of the transit time distribution for a wide range of catchment response characteristics. In combination with reactive tracer time series, this approach can potentially be extended to measure short-term chemical reaction rates at the catchment scale. High-frequency tracer time series from several experimental catchments will be used to demonstrate the utility of the new approach outlined here.
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SSAGES: Software Suite for Advanced General Ensemble Simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian
Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniquesmore » as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.« less
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SSAGES: Software Suite for Advanced General Ensemble Simulations.
Sidky, Hythem; Colón, Yamil J; Helfferich, Julian; Sikora, Benjamin J; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S; Reid, Daniel R; Sevgen, Emre; Thapar, Vikram; Webb, Michael A; Whitmer, Jonathan K; de Pablo, Juan J
2018-01-28
Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.
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SSAGES: Software Suite for Advanced General Ensemble Simulations
NASA Astrophysics Data System (ADS)
Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.
2018-01-01
Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.
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Leveraging Ensemble Dynamical Properties to Prioritize Exoplanet Follow-Up Observations
NASA Astrophysics Data System (ADS)
Ballard, Sarah
2017-01-01
The number of transiting exoplanets now exceeds several thousand, enabling ensemble studies of the dynamical properties of exoplanetary systems. We require a mixture model of dynamical conditions (whether frozen in from formation or sculpted by planet-planet interactions) to recover Kepler's yield of transiting planets. Around M dwarfs, which will be predominate sites of exoplanet follow-up atmospheric study in the next decade, even a modest orbital eccentricity can sterilize a planet. I will describe efforts to link cheap observables, such as number of transiting planets and presence of transit timing variations, to eccentricity and mutual inclination in exoplanet systems. The addition of a second transiting planet, for example, halves the expected orbital eccentricity. For the vast majority of TESS targets, the light curve alone will furnish the sum total of data about the exoplanet. Extracting information about orbital properties from these light curves will help prioritize precious follow-up resources.
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Shchekin, Alexander K; Shabaev, Ilya V; Hellmuth, Olaf
2013-02-07
Thermodynamic and kinetic peculiarities of nucleation, deliquescence and efflorescence transitions in the ensemble of droplets formed on soluble condensation nuclei from a solvent vapor have been considered. The interplay of the effects of solubility and the size of condensation nuclei has been analyzed. Activation barriers for the deliquescence and phase transitions and for the reverse efflorescence transition have been determined as functions of the relative humidity of the vapor-gas atmosphere, initial size, and solubility of condensation nuclei. It has been demonstrated that, upon variations in the relative humidity of the atmosphere, the crossover in thermodynamically stable and unstable variables of the droplet state takes place. The physical meaning of stable and unstable variables has been clarified. The kinetic equations for establishing equilibrium and steady distributions of binary droplets have been solved. The specific times for relaxation, deliquescence and efflorescence transitions have been calculated.
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Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M.
2011-01-01
We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, Transition Path Theory (TPT) for constructing folding pathways and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270K and 566K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the Weighted-Histogram-Analysis Method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (Pfold) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding “tubes”, a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways. PMID:21254767
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Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M
2011-02-17
We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, transition path theory (TPT) for constructing folding pathways, and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270 and 566 K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the weighted-histogram-analysis method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (P(fold)) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding "tubes", a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network, and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways.
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Quantum caustics in resonance-fluorescence trajectories
NASA Astrophysics Data System (ADS)
Naghiloo, M.; Tan, D.; Harrington, P. M.; Lewalle, P.; Jordan, A. N.; Murch, K. W.
2017-11-01
We employ phase-sensitive amplification to perform homodyne detection of the resonance fluorescence from a driven superconducting artificial atom. Entanglement between the emitter and its fluorescence allows us to track the individual quantum state trajectories of the emitter conditioned on the outcomes of the field measurements. We analyze the ensemble properties of these trajectories by considering trajectories that connect specific initial and final states. By applying the stochastic path-integral formalism, we calculate equations of motion for the most-likely path between two quantum states and compare these predicted paths to experimental data. Drawing on the mathematical similarity between the action formalism of the most-likely quantum paths and ray optics, we study the emergence of caustics in quantum trajectories: places where multiple extrema in the stochastic action occur. We observe such multiple most-likely paths in experimental data and find these paths to be in reasonable quantitative agreement with theoretical calculations.
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Ensemble: an Architecture for Mission-Operations Software
NASA Technical Reports Server (NTRS)
Norris, Jeffrey; Powell, Mark; Fox, Jason; Rabe, Kenneth; Shu, IHsiang; McCurdy, Michael; Vera, Alonso
2008-01-01
Ensemble is the name of an open architecture for, and a methodology for the development of, spacecraft mission operations software. Ensemble is also potentially applicable to the development of non-spacecraft mission-operations- type software. Ensemble capitalizes on the strengths of the open-source Eclipse software and its architecture to address several issues that have arisen repeatedly in the development of mission-operations software: Heretofore, mission-operations application programs have been developed in disparate programming environments and integrated during the final stages of development of missions. The programs have been poorly integrated, and it has been costly to develop, test, and deploy them. Users of each program have been forced to interact with several different graphical user interfaces (GUIs). Also, the strategy typically used in integrating the programs has yielded serial chains of operational software tools of such a nature that during use of a given tool, it has not been possible to gain access to the capabilities afforded by other tools. In contrast, the Ensemble approach offers a low-risk path towards tighter integration of mission-operations software tools.
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Explore Stochastic Instabilities of Periodic Points by Transition Path Theory
NASA Astrophysics Data System (ADS)
Cao, Yu; Lin, Ling; Zhou, Xiang
2016-06-01
We consider the noise-induced transitions from a linearly stable periodic orbit consisting of T periodic points in randomly perturbed discrete logistic map. Traditional large deviation theory and asymptotic analysis at small noise limit cannot distinguish the quantitative difference in noise-induced stochastic instabilities among the T periodic points. To attack this problem, we generalize the transition path theory to the discrete-time continuous-space stochastic process. In our first criterion to quantify the relative instability among T periodic points, we use the distribution of the last passage location related to the transitions from the whole periodic orbit to a prescribed disjoint set. This distribution is related to individual contributions to the transition rate from each periodic points. The second criterion is based on the competency of the transition paths associated with each periodic point. Both criteria utilize the reactive probability current in the transition path theory. Our numerical results for the logistic map reveal the transition mechanism of escaping from the stable periodic orbit and identify which periodic point is more prone to lose stability so as to make successful transitions under random perturbations.
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Transition paths in single-molecule force spectroscopy
NASA Astrophysics Data System (ADS)
Cossio, Pilar; Hummer, Gerhard; Szabo, Attila
2018-03-01
In a typical single-molecule force spectroscopy experiment, the ends of the molecule of interest are connected by long polymer linkers to a pair of mesoscopic beads trapped in the focus of two laser beams. At constant force load, the total extension, i.e., the end-to-end distance of the molecule plus linkers, is measured as a function of time. In the simplest systems, the measured extension fluctuates about two values characteristic of folded and unfolded states, with occasional transitions between them. We have recently shown that molecular (un)folding rates can be recovered from such trajectories, with a small linker correction, as long as the characteristic time of the bead fluctuations is shorter than the residence time in the unfolded (folded) state. Here, we show that accurate measurements of the molecular transition path times require an even faster apparatus response. Transition paths, the trajectory segments in which the molecule (un)folds, are properly resolved only if the beads fluctuate more rapidly than the end-to-end distance of the molecule. Therefore, over a wide regime, the measured rates may be meaningful but not the transition path times. Analytic expressions for the measured mean transition path times are obtained for systems diffusing anisotropically on a two-dimensional free energy surface. The transition path times depend on the properties both of the molecule and of the pulling device.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Aleksandrov, I. A., E-mail: Aleksandrov@isp.nsc.ru; Mansurov, V. G.; Zhuravlev, K. S.
2016-08-15
The carrier recombination dynamics in an ensemble of GaN/AlN quantum dots is studied. The model proposed for describing this dynamics takes into account the transition of carriers between quantum dots and defects in a matrix. Comparison of the experimental and calculated photoluminescence decay curves shows that the interaction between quantum dots and defects slows down photoluminescence decay in the ensemble of GaN/AlN quantum dots.
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NASA Astrophysics Data System (ADS)
Maleki, Yusef; Zheltikov, Aleksei M.
2018-01-01
An ensemble of nitrogen-vacancy (NV) centers coupled to a circuit QED device is shown to enable an efficient, high-fidelity generation of high-N00N states. Instead of first creating entanglement and then increasing the number of entangled particles N , our source of high-N00N states first prepares a high-N Fock state in one of the NV ensembles and then entangles it to the rest of the system. With such a strategy, high-N N00N states can be generated in just a few operational steps with an extraordinary fidelity. Once prepared, such a state can be stored over a longer period of time due to the remarkably long coherence time of NV centers.
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Four-Wave Mixing Spectroscopy of Quantum Dot Molecules
NASA Astrophysics Data System (ADS)
Sitek, A.; Machnikowski, P.
2007-08-01
We study theoretically the nonlinear four-wave mixing response of an ensemble of coupled pairs of quantum dots (quantum dot molecules). We discuss the shape of the echo signal depending on the parameters of the ensemble: the statistics of transition energies and the degree of size correlations between the dots forming the molecules.
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Path Finding on High-Dimensional Free Energy Landscapes
NASA Astrophysics Data System (ADS)
Díaz Leines, Grisell; Ensing, Bernd
2012-07-01
We present a method for determining the average transition path and the free energy along this path in the space of selected collective variables. The formalism is based upon a history-dependent bias along a flexible path variable within the metadynamics framework but with a trivial scaling of the cost with the number of collective variables. Controlling the sampling of the orthogonal modes recovers the average path and the minimum free energy path as the limiting cases. The method is applied to resolve the path and the free energy of a conformational transition in alanine dipeptide.
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NASA Astrophysics Data System (ADS)
Li, Gu-Qiang; Mo, Jie-Xiong
2016-06-01
The phase transition of a four-dimensional charged AdS black hole solution in the R +f (R ) gravity with constant curvature is investigated in the grand canonical ensemble, where we find novel characteristics quite different from that in the canonical ensemble. There exists no critical point for T -S curve while in former research critical point was found for both the T -S curve and T -r+ curve when the electric charge of f (R ) black holes is kept fixed. Moreover, we derive the explicit expression for the specific heat, the analog of volume expansion coefficient and isothermal compressibility coefficient when the electric potential of f (R ) AdS black hole is fixed. The specific heat CΦ encounters a divergence when 0 <Φ b . This finding also differs from the result in the canonical ensemble, where there may be two, one or no divergence points for the specific heat CQ . To examine the phase structure newly found in the grand canonical ensemble, we appeal to the well-known thermodynamic geometry tools and derive the analytic expressions for both the Weinhold scalar curvature and Ruppeiner scalar curvature. It is shown that they diverge exactly where the specific heat CΦ diverges.
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Computation of rare transitions in the barotropic quasi-geostrophic equations
NASA Astrophysics Data System (ADS)
Laurie, Jason; Bouchet, Freddy
2015-01-01
We investigate the theoretical and numerical computation of rare transitions in simple geophysical turbulent models. We consider the barotropic quasi-geostrophic and two-dimensional Navier-Stokes equations in regimes where bistability between two coexisting large-scale attractors exist. By means of large deviations and instanton theory with the use of an Onsager-Machlup path integral formalism for the transition probability, we show how one can directly compute the most probable transition path between two coexisting attractors analytically in an equilibrium (Langevin) framework and numerically otherwise. We adapt a class of numerical optimization algorithms known as minimum action methods to simple geophysical turbulent models. We show that by numerically minimizing an appropriate action functional in a large deviation limit, one can predict the most likely transition path for a rare transition between two states. By considering examples where theoretical predictions can be made, we show that the minimum action method successfully predicts the most likely transition path. Finally, we discuss the application and extension of such numerical optimization schemes to the computation of rare transitions observed in direct numerical simulations and experiments and to other, more complex, turbulent systems.
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Order and disorder in coupled metronome systems
NASA Astrophysics Data System (ADS)
Boda, Sz.; Davidova, L.; Néda, Z.
2014-04-01
Metronomes placed on a smoothly rotating disk are used for exemplifying order-disorder type phase-transitions. The ordered phase corresponds to spontaneously synchronized beats, while the disordered state is when the metronomes swing in unsynchronized manner. Using a given metronome ensemble, we propose several methods for switching between ordered and disordered states. The system is studied by controlled experiments and a realistic model. The model reproduces the experimental results, and allows to study large ensembles with good statistics. Finite-size effects and the increased fluctuation in the vicinity of the phase-transition point are also successfully reproduced.
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Kingsley, Laura J.; Lill, Markus A.
2014-01-01
Computational prediction of ligand entry and egress paths in proteins has become an emerging topic in computational biology and has proven useful in fields such as protein engineering and drug design. Geometric tunnel prediction programs, such as Caver3.0 and MolAxis, are computationally efficient methods to identify potential ligand entry and egress routes in proteins. Although many geometric tunnel programs are designed to accommodate a single input structure, the increasingly recognized importance of protein flexibility in tunnel formation and behavior has led to the more widespread use of protein ensembles in tunnel prediction. However, there has not yet been an attempt to directly investigate the influence of ensemble size and composition on geometric tunnel prediction. In this study, we compared tunnels found in a single crystal structure to ensembles of various sizes generated using different methods on both the apo and holo forms of cytochrome P450 enzymes CYP119, CYP2C9, and CYP3A4. Several protein structure clustering methods were tested in an attempt to generate smaller ensembles that were capable of reproducing the data from larger ensembles. Ultimately, we found that by including members from both the apo and holo data sets, we could produce ensembles containing less than 15 members that were comparable to apo or holo ensembles containing over 100 members. Furthermore, we found that, in the absence of either apo or holo crystal structure data, pseudo-apo or –holo ensembles (e.g. adding ligand to apo protein throughout MD simulations) could be used to resemble the structural ensembles of the corresponding apo and holo ensembles, respectively. Our findings not only further highlight the importance of including protein flexibility in geometric tunnel prediction, but also suggest that smaller ensembles can be as capable as larger ensembles at capturing many of the protein motions important for tunnel prediction at a lower computational cost. PMID:24956479
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Analyses and forecasts of a tornadic supercell outbreak using a 3DVAR system ensemble
NASA Astrophysics Data System (ADS)
Zhuang, Zhaorong; Yussouf, Nusrat; Gao, Jidong
2016-05-01
As part of NOAA's "Warn-On-Forecast" initiative, a convective-scale data assimilation and prediction system was developed using the WRF-ARW model and ARPS 3DVAR data assimilation technique. The system was then evaluated using retrospective short-range ensemble analyses and probabilistic forecasts of the tornadic supercell outbreak event that occurred on 24 May 2011 in Oklahoma, USA. A 36-member multi-physics ensemble system provided the initial and boundary conditions for a 3-km convective-scale ensemble system. Radial velocity and reflectivity observations from four WSR-88Ds were assimilated into the ensemble using the ARPS 3DVAR technique. Five data assimilation and forecast experiments were conducted to evaluate the sensitivity of the system to data assimilation frequencies, in-cloud temperature adjustment schemes, and fixed- and mixed-microphysics ensembles. The results indicated that the experiment with 5-min assimilation frequency quickly built up the storm and produced a more accurate analysis compared with the 10-min assimilation frequency experiment. The predicted vertical vorticity from the moist-adiabatic in-cloud temperature adjustment scheme was larger in magnitude than that from the latent heat scheme. Cycled data assimilation yielded good forecasts, where the ensemble probability of high vertical vorticity matched reasonably well with the observed tornado damage path. Overall, the results of the study suggest that the 3DVAR analysis and forecast system can provide reasonable forecasts of tornadic supercell storms.
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Hernández, Griselda; Anderson, Janet S.; LeMaster, David M.
2012-01-01
The acute sensitivity to conformation exhibited by amide hydrogen exchange reactivity provides a valuable test for the physical accuracy of model ensembles developed to represent the Boltzmann distribution of the protein native state. A number of molecular dynamics studies of ubiquitin have predicted a well-populated transition in the tight turn immediately preceding the primary site of proteasome-directed polyubiquitylation Lys 48. Amide exchange reactivity analysis demonstrates that this transition is 103-fold rarer than these predictions. More strikingly, for the most populated novel conformational basin predicted from a recent 1 ms MD simulation of bovine pancreatic trypsin inhibitor (at 13% of total), experimental hydrogen exchange data indicates a population below 10−6. The most sophisticated efforts to directly incorporate experimental constraints into the derivation of model protein ensembles have been applied to ubiquitin, as illustrated by three recently deposited studies (PDB codes 2NR2, 2K39 and 2KOX). Utilizing the extensive set of experimental NOE constraints, each of these three ensembles yields a modestly more accurate prediction of the exchange rates for the highly exposed amides than does a standard unconstrained molecular simulation. However, for the less frequently exposed amide hydrogens, the 2NR2 ensemble offers no improvement in rate predictions as compared to the unconstrained MD ensemble. The other two NMR-constrained ensembles performed markedly worse, either underestimating (2KOX) or overestimating (2K39) the extent of conformational diversity. PMID:22425325
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Maxwell's equal area law for black holes in power Maxwell invariant
NASA Astrophysics Data System (ADS)
Li, Huai-Fan; Guo, Xiong-ying; Zhao, Hui-Hua; Zhao, Ren
2017-08-01
In this paper, we consider the phase transition of black hole in power Maxwell invariant by means of Maxwell's equal area law. First, we review and study the analogy of nonlinear charged black hole solutions with the Van der Waals gas-liquid system in the extended phase space, and obtain isothermal P- v diagram. Then, using the Maxwell's equal area law we study the phase transition of AdS black hole with different temperatures. Finally, we extend the method to the black hole in the canonical (grand canonical) ensemble in which charge (potential) is fixed at infinity. Interestingly, we find the phase transition occurs in the both ensembles. We also study the effect of the parameters of the black hole on the two-phase coexistence. The results show that the black hole may go through a small-large phase transition similar to those of usual non-gravity thermodynamic systems.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Song, Xuehang; Chen, Xingyuan; Ye, Ming
2015-07-01
This study develops a new framework of facies-based data assimilation for characterizing spatial distribution of hydrofacies and estimating their associated hydraulic properties. This framework couples ensemble data assimilation with transition probability-based geostatistical model via a parameterization based on a level set function. The nature of ensemble data assimilation makes the framework efficient and flexible to be integrated with various types of observation data. The transition probability-based geostatistical model keeps the updated hydrofacies distributions under geological constrains. The framework is illustrated by using a two-dimensional synthetic study that estimates hydrofacies spatial distribution and permeability in each hydrofacies from transient head data.more » Our results show that the proposed framework can characterize hydrofacies distribution and associated permeability with adequate accuracy even with limited direct measurements of hydrofacies. Our study provides a promising starting point for hydrofacies delineation in complex real problems.« less
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Laser transit anemometer software development program
NASA Technical Reports Server (NTRS)
Abbiss, John B.
1989-01-01
Algorithms were developed for the extraction of two components of mean velocity, standard deviation, and the associated correlation coefficient from laser transit anemometry (LTA) data ensembles. The solution method is based on an assumed two-dimensional Gaussian probability density function (PDF) model of the flow field under investigation. The procedure consists of transforming the data ensembles from the data acquisition domain (consisting of time and angle information) to the velocity space domain (consisting of velocity component information). The mean velocity results are obtained from the data ensemble centroid. Through a least squares fitting of the transformed data to an ellipse representing the intersection of a plane with the PDF, the standard deviations and correlation coefficient are obtained. A data set simulation method is presented to test the data reduction process. Results of using the simulation system with a limited test matrix of input values is also given.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cheng Jing; Huang Guoxiang; State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062
2011-05-15
We propose a scheme to realize a transition from delocalization to localization of light waves via electromagnetically induced transparency. The system we suggested is a resonant cold atomic ensemble having N configuration, with a control field consisting of two pairs of laser beams with different cross angles, which produce an electromagnetically induced quasiperiodic waveguide (EIQPW) for the propagation of a signal field. By appropriately tuning the incommensurate rate or relative modulation strength between the two pairs of control-field components, the signal field can exhibit the delocalization-localization transition as it transports inside the atomic ensemble. The delocalization-localization transition point is determinedmore » and the propagation property of the signal field is studied in detail. Our work provides a way of realizing wave localization via atomic coherence, which is quite different from the conventional, off-resonant mechanism-based Aubry-Andre model, and the great controllability of the EIQPW also allows an easy manipulation of the delocalization-localization transition.« less
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NASA Astrophysics Data System (ADS)
Isoguchi, O.; Matsui, K.; Kamachi, M.; Usui, N.; Miyazawa, Y.; Ishikawa, Y.; Hirose, N.
2017-12-01
Several operational ocean assimilation models are currently available for the Northwestern Pacific and surrounding marginal seas. One of the main targets is predicting the Kuroshio/Kuroshio Extension, which have an impact not only on social activities, such as fishery and ship routing, but also on local weather. There is a demand to assess their quality comprehensively and make the best out the available products. In the present study, several ocean data assimilation products and their multi-ensemble product were assessed by comparing with satellite-derived sea surface temperature (SST), sea surface height (SSH), and in-situ hydrographic sections. The Kuroshio axes were also computed from the surface currents of these products and were compared with the Kuroshio Axis data produced analyzing satellite-SST, SSH, and in-situ observations by Marine Information Research Center (MIRC). The multi-model ensemble products generally showed the best accuracy in terms of the comparisons with the satellite-derived SST and SSH. On the other hand, the ensemble products didn't result in the best one in the comparison with the hydrographic sections. It is thus suggested that the multi-model ensemble works efficiently for the horizontally 2D parameters for which each assimilation product tends to have random errors while it does not work well for the vertical 2D comparisons for which it tends to have bias errors with respect to in-situ data. In the assessment with the Kuroshio Axis Data, some products showed more energetic behavior than the Kuroshio Axis data, resulting in the large path errors which are defined as a ratio between an area surrounded by the reference and model-derived ones and a path length. It is however not determined which are real, because in-situ observations are still lacking to resolve energetic Kuroshio behavior even though the Kuroshio is one of the strongest current.
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Importance sampling large deviations in nonequilibrium steady states. I.
Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T
2018-03-28
Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.
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Importance sampling large deviations in nonequilibrium steady states. I
NASA Astrophysics Data System (ADS)
Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.
2018-03-01
Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.
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A brief history of the introduction of generalized ensembles to Markov chain Monte Carlo simulations
NASA Astrophysics Data System (ADS)
Berg, Bernd A.
2017-03-01
The most efficient weights for Markov chain Monte Carlo calculations of physical observables are not necessarily those of the canonical ensemble. Generalized ensembles, which do not exist in nature but can be simulated on computers, lead often to a much faster convergence. In particular, they have been used for simulations of first order phase transitions and for simulations of complex systems in which conflicting constraints lead to a rugged free energy landscape. Starting off with the Metropolis algorithm and Hastings' extension, I present a minireview which focuses on the explosive use of generalized ensembles in the early 1990s. Illustrations are given, which range from spin models to peptides.
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Three key residues form a critical contact network in a protein folding transition state
NASA Astrophysics Data System (ADS)
Vendruscolo, Michele; Paci, Emanuele; Dobson, Christopher M.; Karplus, Martin
2001-02-01
Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements-which determine the role of individual residues in stabilizing the transition state-as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6Å from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.
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Embedded random matrix ensembles from nuclear structure and their recent applications
NASA Astrophysics Data System (ADS)
Kota, V. K. B.; Chavda, N. D.
Embedded random matrix ensembles generated by random interactions (of low body rank and usually two-body) in the presence of a one-body mean field, introduced in nuclear structure physics, are now established to be indispensable in describing statistical properties of a large number of isolated finite quantum many-particle systems. Lie algebra symmetries of the interactions, as identified from nuclear shell model and the interacting boson model, led to the introduction of a variety of embedded ensembles (EEs). These ensembles with a mean field and chaos generating two-body interaction generate in three different stages, delocalization of wave functions in the Fock space of the mean-field basis states. The last stage corresponds to what one may call thermalization and complex nuclei, as seen from many shell model calculations, lie in this region. Besides briefly describing them, their recent applications to nuclear structure are presented and they are (i) nuclear level densities with interactions; (ii) orbit occupancies; (iii) neutrinoless double beta decay nuclear transition matrix elements as transition strengths. In addition, their applications are also presented briefly that go beyond nuclear structure and they are (i) fidelity, decoherence, entanglement and thermalization in isolated finite quantum systems with interactions; (ii) quantum transport in disordered networks connected by many-body interactions with centrosymmetry; (iii) semicircle to Gaussian transition in eigenvalue densities with k-body random interactions and its relation to the Sachdev-Ye-Kitaev (SYK) model for majorana fermions.
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Helmholtz and Gibbs ensembles, thermodynamic limit and bistability in polymer lattice models
NASA Astrophysics Data System (ADS)
Giordano, Stefano
2017-12-01
Representing polymers by random walks on a lattice is a fruitful approach largely exploited to study configurational statistics of polymer chains and to develop efficient Monte Carlo algorithms. Nevertheless, the stretching and the folding/unfolding of polymer chains within the Gibbs (isotensional) and the Helmholtz (isometric) ensembles of the statistical mechanics have not been yet thoroughly analysed by means of the lattice methodology. This topic, motivated by the recent introduction of several single-molecule force spectroscopy techniques, is investigated in the present paper. In particular, we analyse the force-extension curves under the Gibbs and Helmholtz conditions and we give a proof of the ensembles equivalence in the thermodynamic limit for polymers represented by a standard random walk on a lattice. Then, we generalize these concepts for lattice polymers that can undergo conformational transitions or, equivalently, for chains composed of bistable or two-state elements (that can be either folded or unfolded). In this case, the isotensional condition leads to a plateau-like force-extension response, whereas the isometric condition causes a sawtooth-like force-extension curve, as predicted by numerous experiments. The equivalence of the ensembles is finally proved also for lattice polymer systems exhibiting conformational transitions.
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The Origins of the "Fanga" Dance
ERIC Educational Resources Information Center
Damm, Robert J.
2015-01-01
The "fanga" is a dance taught throughout the United States to children in elementary music classes, students in African dance classes, teachers in multicultural workshops, and professional dancers in touring ensembles. Although the history of the fanga is a path overgrown with myth, this article offers information about the dance's…
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Jarzynski equality in the context of maximum path entropy
NASA Astrophysics Data System (ADS)
González, Diego; Davis, Sergio
2017-06-01
In the global framework of finding an axiomatic derivation of nonequilibrium Statistical Mechanics from fundamental principles, such as the maximum path entropy - also known as Maximum Caliber principle -, this work proposes an alternative derivation of the well-known Jarzynski equality, a nonequilibrium identity of great importance today due to its applications to irreversible processes: biological systems (protein folding), mechanical systems, among others. This equality relates the free energy differences between two equilibrium thermodynamic states with the work performed when going between those states, through an average over a path ensemble. In this work the analysis of Jarzynski's equality will be performed using the formalism of inference over path space. This derivation highlights the wide generality of Jarzynski's original result, which could even be used in non-thermodynamical settings such as social systems, financial and ecological systems.
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Ovchinnikov, Victor; Karplus, Martin; Vanden-Eijnden, Eric
2011-01-01
A set of techniques developed under the umbrella of the string method is used in combination with all-atom molecular dynamics simulations to analyze the conformation change between the prepowerstroke (PPS) and rigor (R) structures of the converter domain of myosin VI. The challenges specific to the application of these techniques to such a large and complex biomolecule are addressed in detail. These challenges include (i) identifying a proper set of collective variables to apply the string method, (ii) finding a suitable initial string, (iii) obtaining converged profiles of the free energy along the transition path, (iv) validating and interpreting the free energy profiles, and (v) computing the mean first passage time of the transition. A detailed description of the PPS↔R transition in the converter domain of myosin VI is obtained, including the transition path, the free energy along the path, and the rates of interconversion. The methodology developed here is expected to be useful more generally in studies of conformational transitions in complex biomolecules. PMID:21361558
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Enzymatic reaction paths as determined by transition path sampling
NASA Astrophysics Data System (ADS)
Masterson, Jean Emily
Enzymes are biological catalysts capable of enhancing the rates of chemical reactions by many orders of magnitude as compared to solution chemistry. Since the catalytic power of enzymes routinely exceeds that of the best artificial catalysts available, there is much interest in understanding the complete nature of chemical barrier crossing in enzymatic reactions. Two specific questions pertaining to the source of enzymatic rate enhancements are investigated in this work. The first is the issue of how fast protein motions of an enzyme contribute to chemical barrier crossing. Our group has previously identified sub-picosecond protein motions, termed promoting vibrations (PVs), that dynamically modulate chemical transformation in several enzymes. In the case of human heart lactate dehydrogenase (hhLDH), prior studies have shown that a specific axis of residues undergoes a compressional fluctuation towards the active site, decreasing a hydride and a proton donor--acceptor distance on a sub-picosecond timescale to promote particle transfer. To more thoroughly understand the contribution of this dynamic motion to the enzymatic reaction coordinate of hhLDH, we conducted transition path sampling (TPS) using four versions of the enzymatic system: a wild type enzyme with natural isotopic abundance; a heavy enzyme where all the carbons, nitrogens, and non-exchangeable hydrogens were replaced with heavy isotopes; and two versions of the enzyme with mutations in the axis of PV residues. We generated four separate ensembles of reaction paths and analyzed each in terms of the reaction mechanism, time of barrier crossing, dynamics of the PV, and residues involved in the enzymatic reaction coordinate. We found that heavy isotopic substitution of hhLDH altered the sub-picosecond dynamics of the PV, changed the favored reaction mechanism, dramatically increased the time of barrier crossing, but did not have an effect on the specific residues involved in the PV. In the mutant systems, we observed changes in the reaction mechanism and altered contributions of the mutated residues to the enzymatic reaction coordinate, but we did not detect a substantial change in the time of barrier crossing. These results confirm the importance of maintaining the dynamics and structural scaffolding of the hhLDH PV in order to facilitate facile barrier passage. We also utilized TPS to investigate the possible role of fast protein dynamics in the enzymatic reaction coordinate of human dihydrofolate reductase (hsDHFR). We found that sub-picosecond dynamics of hsDHFR do contribute to the reaction coordinate, whereas this is not the case in the E. coli version of the enzyme. This result indicates a shift in the DHFR family to a more dynamic version of catalysis. The second inquiry we addressed in this thesis regarding enzymatic barrier passage concerns the variability of paths through reactive phase space for a given enzymatic reaction. We further investigated the hhLDH-catalyzed reaction using a high-perturbation TPS algorithm. Though we saw that alternate reaction paths were possible, the dominant reaction path we observed corresponded to that previously elucidated in prior hhLDH TPS studies. Since the additional reaction paths we observed were likely high-energy, these results indicate that only the dominant reaction path contributes significantly to the overall reaction rate. In conclusion, we show that the enzymes hhLDH and hsDHFR exhibit paths through reactive phase space where fast protein motions are involved in the enzymatic reaction coordinate and exhibit a non-negligible contribution to chemical barrier crossing.
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High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study
Seshasayee, Aswin Sai Narain
2005-01-01
Background Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns. Results High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg) and Root Mean Square Deviation (RMSD) have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles. Conclusion Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE), shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here. PMID:15760474
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NASA Technical Reports Server (NTRS)
Buchard, Virginie; Da Silva, Arlindo; Todling, Ricardo
2017-01-01
In the GEOS near real-time system, as well as in MERRA-2 which is the latest reanalysis produced at NASAs Global Modeling and Assimilation Office(GMAO), the assimilation of aerosol observations is performed by means of a so-called analysis splitting method. In line with the transition of the GEOS meteorological data assimilation system to a hybrid Ensemble-Variational formulation, we are updating the aerosol component of our assimilation system to an ensemble square root filter(EnSRF; Whitaker and Hamill (2002)) type of scheme.We present a summary of our preliminary results of the assimilation of column integrated aerosol observations (Aerosol Optical Depth; AOD) using an Ensemble Square Root Filters (EnSRF) scheme and the ensemble members produced routinely by the meteorological assimilation.
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Symmetry Transition Preserving Chirality in QCD: A Versatile Random Matrix Model
NASA Astrophysics Data System (ADS)
Kanazawa, Takuya; Kieburg, Mario
2018-06-01
We consider a random matrix model which interpolates between the chiral Gaussian unitary ensemble and the Gaussian unitary ensemble while preserving chiral symmetry. This ensemble describes flavor symmetry breaking for staggered fermions in 3D QCD as well as in 4D QCD at high temperature or in 3D QCD at a finite isospin chemical potential. Our model is an Osborn-type two-matrix model which is equivalent to the elliptic ensemble but we consider the singular value statistics rather than the complex eigenvalue statistics. We report on exact results for the partition function and the microscopic level density of the Dirac operator in the ɛ regime of QCD. We compare these analytical results with Monte Carlo simulations of the matrix model.
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NASA Astrophysics Data System (ADS)
Gross, D. H. E.
1997-01-01
This review is addressed to colleagues working in different fields of physics who are interested in the concepts of microcanonical thermodynamics, its relation and contrast to ordinary, canonical or grandcanonical thermodynamics, and to get a first taste of the wide area of new applications of thermodynamical concepts like hot nuclei, hot atomic clusters and gravitating systems. Microcanonical thermodynamics describes how the volume of the N-body phase space depends on the globally conserved quantities like energy, angular momentum, mass, charge, etc. Due to these constraints the microcanonical ensemble can behave quite differently from the conventional, canonical or grandcanonical ensemble in many important physical systems. Microcanonical systems become inhomogeneous at first-order phase transitions, or with rising energy, or with external or internal long-range forces like Coulomb, centrifugal or gravitational forces. Thus, fragmentation of the system into a spatially inhomogeneous distribution of various regions of different densities and/or of different phases is a genuine characteristic of the microcanonical ensemble. In these cases which are realized by the majority of realistic systems in nature, the microcanonical approach is the natural statistical description. We investigate this most fundamental form of thermodynamics in four different nontrivial physical cases: (I) Microcanonical phase transitions of first and second order are studied within the Potts model. The total energy per particle is a nonfluctuating order parameter which controls the phase which the system is in. In contrast to the canonical form the microcanonical ensemble allows to tune the system continuously from one phase to the other through the region of coexisting phases by changing the energy smoothly. The configurations of coexisting phases carry important informations about the nature of the phase transition. This is more remarkable as the canonical ensemble is blind against these configurations. It is shown that the three basic quantities which specify a phase transition of first order - Transition temperature, latent heat, and interphase surface entropy - can be well determined for finite systems from the caloric equation of state T( E) in the coexistence region. Their values are already for a lattice of only ~ 30 ∗ 30 spins close to the ones of the corresponding infinite system. The significance of the backbending of the caloric equation of state T( E) is clarified. It is the signal for a phase transition of first order in a finite isolated system. (II) Fragmentation is shown to be a specific and generic phase transition of finite systems. The caloric equation of state T( E) for hot nuclei is calculated. The phase transition towards fragmentation can unambiguously be identified by the anomalies in T( E). As microcanonical thermodynamics is a full N-body theory it determines all many-body correlations as well. Consequently, various statistical multi-fragment correlations are investigated which give insight into the details of the equilibration mechanism. (III) Fragmentation of neutral and multiply charged atomic clusters is the next example of a realistic application of microcanonical thermodynamics. Our simulation method, microcanonical Metropolis Monte Carlo, combines the explicit microscopic treatment of the fragmentational degrees of freedom with the implicit treatment of the internal degrees of freedom of the fragments described by the experimental bulk specific heat. This micro-macro approach allows us to study the fragmentation of also larger fragments. Characteristic details of the fission of multiply charged metal clusters find their explanation by the different bulk properties. (IV) Finally, the fragmentation of strongly rotating nuclei is discussed as an example for a microcanonical ensemble under the action of a two-dimensional repulsive force.
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NASA Astrophysics Data System (ADS)
Bizheva, Kostadinka K.; Siegel, Andy M.; Boas, David A.
1998-12-01
We used low coherence interferometry to measure Brownian motion within highly scattering random media. A coherence gate was applied to resolve the optical path-length distribution and to separate ballistic from diffusive light. Our experimental analysis provides details on the transition from single scattering to light diffusion and its dependence on the system parameters. We found that the transition to the light diffusion regime occurs at shorter path lengths for media with higher scattering anisotropy or for larger numerical aperture of the focusing optics.
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An ensemble-based approach for breast mass classification in mammography images
NASA Astrophysics Data System (ADS)
Ribeiro, Patricia B.; Papa, João. P.; Romero, Roseli A. F.
2017-03-01
Mammography analysis is an important tool that helps detecting breast cancer at the very early stages of the disease, thus increasing the quality of life of hundreds of thousands of patients worldwide. In Computer-Aided Detection systems, the identification of mammograms with and without masses (without clinical findings) is highly needed to reduce the false positive rates regarding the automatic selection of regions of interest that may contain some suspicious content. In this work, the introduce a variant of the Optimum-Path Forest (OPF) classifier for breast mass identification, as well as we employed an ensemble-based approach that can enhance the effectiveness of individual classifiers aiming at dealing with the aforementioned purpose. The experimental results also comprise the naïve OPF and a traditional neural network, being the most accurate results obtained through the ensemble of classifiers, with an accuracy nearly to 86%.
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NASA Astrophysics Data System (ADS)
Bogomolov, Sergey A.; Slepnev, Andrei V.; Strelkova, Galina I.; Schöll, Eckehard; Anishchenko, Vadim S.
2017-02-01
We explore the bifurcation transition from coherence to incoherence in ensembles of nonlocally coupled chaotic systems. It is firstly shown that two types of chimera states, namely, amplitude and phase, can be found in a network of coupled logistic maps, while only amplitude chimera states can be observed in a ring of continuous-time chaotic systems. We reveal a bifurcation mechanism by analyzing the evolution of space-time profiles and the coupling function with varying coupling coefficient and formulate the necessary and sufficient conditions for realizing the chimera states in the ensembles.
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NASA Astrophysics Data System (ADS)
Zhumagulov, Yaroslav V.; Krasavin, Andrey V.; Kashurnikov, Vladimir A.
2018-05-01
The method is developed for calculation of electronic properties of an ensemble of metal nanoclusters with the use of cluster perturbation theory. This method is applied to the system of gold nanoclusters. The Greens function of single nanocluster is obtained by ab initio calculations within the framework of the density functional theory, and then is used in Dyson equation to group nanoclusters together and to compute the Greens function as well as the electron density of states of the whole ensemble. The transition from insulator state of a single nanocluster to metallic state of bulk gold is observed.
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Dissipation induced asymmetric steering of distant atomic ensembles
NASA Astrophysics Data System (ADS)
Cheng, Guangling; Tan, Huatang; Chen, Aixi
2018-04-01
The asymmetric steering effects of separated atomic ensembles denoted by the effective bosonic modes have been explored by the means of quantum reservoir engineering in the setting of the cascaded cavities, in each of which an atomic ensemble is involved. It is shown that the steady-state asymmetric steering of the mesoscopic objects is unconditionally achieved via the dissipation of the cavities, by which the nonlocal interaction occurs between two atomic ensembles, and the direction of steering could be easily controlled through variation of certain tunable system parameters. One advantage of the present scheme is that it could be rather robust against parameter fluctuations, and does not require the accurate control of evolution time and the original state of the system. Furthermore, the double-channel Raman transitions between the long-lived atomic ground states are used and the atomic ensembles act as the quantum network nodes, which makes our scheme insensitive to the collective spontaneous emission of atoms.
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Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active Sites*
Honaker, Matthew T.; Acchione, Mauro; Zhang, Wei; Mannervik, Bengt; Atkins, William M.
2013-01-01
The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning “induced fit” versus “conformational selection” has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1–1 (GSTA1–1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1–1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that “local” molten globule behavior optimizes detoxication enzymes. PMID:23649628
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Ensemble of Transition State Structures for the Cis-Trans Isomerization of N-Methylacetamide
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mantz, Yves A.; Branduardi, Davide; Bussi, Giovanni
2009-09-17
The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verifiedmore » by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms.« less
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Strong diffusion formulation of Markov chain ensembles and its optimal weaker reductions
NASA Astrophysics Data System (ADS)
Güler, Marifi
2017-10-01
Two self-contained diffusion formulations, in the form of coupled stochastic differential equations, are developed for the temporal evolution of state densities over an ensemble of Markov chains evolving independently under a common transition rate matrix. Our first formulation derives from Kurtz's strong approximation theorem of density-dependent Markov jump processes [Stoch. Process. Their Appl. 6, 223 (1978), 10.1016/0304-4149(78)90020-0] and, therefore, strongly converges with an error bound of the order of lnN /N for ensemble size N . The second formulation eliminates some fluctuation variables, and correspondingly some noise terms, within the governing equations of the strong formulation, with the objective of achieving a simpler analytic formulation and a faster computation algorithm when the transition rates are constant or slowly varying. There, the reduction of the structural complexity is optimal in the sense that the elimination of any given set of variables takes place with the lowest attainable increase in the error bound. The resultant formulations are supported by numerical simulations.
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ERIC Educational Resources Information Center
Murphy, Sean
2013-01-01
The saxophone section of a wind ensemble can easily be one of the most frustrating to work with when it comes to producing a clear, characteristic tone. Sometimes, the road to an improved sound can be a long path of daily diligence and practice; however, there are many quicker solutions that will drastically improve a student's tone. This article…
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Temporal Processing in the Visual Cortex of the Awake and Anesthetized Rat.
Aasebø, Ida E J; Lepperød, Mikkel E; Stavrinou, Maria; Nøkkevangen, Sandra; Einevoll, Gaute; Hafting, Torkel; Fyhn, Marianne
2017-01-01
The activity pattern and temporal dynamics within and between neuron ensembles are essential features of information processing and believed to be profoundly affected by anesthesia. Much of our general understanding of sensory information processing, including computational models aimed at mathematically simulating sensory information processing, rely on parameters derived from recordings conducted on animals under anesthesia. Due to the high variety of neuronal subtypes in the brain, population-based estimates of the impact of anesthesia may conceal unit- or ensemble-specific effects of the transition between states. Using chronically implanted tetrodes into primary visual cortex (V1) of rats, we conducted extracellular recordings of single units and followed the same cell ensembles in the awake and anesthetized states. We found that the transition from wakefulness to anesthesia involves unpredictable changes in temporal response characteristics. The latency of single-unit responses to visual stimulation was delayed in anesthesia, with large individual variations between units. Pair-wise correlations between units increased under anesthesia, indicating more synchronized activity. Further, the units within an ensemble show reproducible temporal activity patterns in response to visual stimuli that is changed between states, suggesting state-dependent sequences of activity. The current dataset, with recordings from the same neural ensembles across states, is well suited for validating and testing computational network models. This can lead to testable predictions, bring a deeper understanding of the experimental findings and improve models of neural information processing. Here, we exemplify such a workflow using a Brunel network model.
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Temporal Processing in the Visual Cortex of the Awake and Anesthetized Rat
Aasebø, Ida E. J.; Stavrinou, Maria; Nøkkevangen, Sandra; Einevoll, Gaute
2017-01-01
Abstract The activity pattern and temporal dynamics within and between neuron ensembles are essential features of information processing and believed to be profoundly affected by anesthesia. Much of our general understanding of sensory information processing, including computational models aimed at mathematically simulating sensory information processing, rely on parameters derived from recordings conducted on animals under anesthesia. Due to the high variety of neuronal subtypes in the brain, population-based estimates of the impact of anesthesia may conceal unit- or ensemble-specific effects of the transition between states. Using chronically implanted tetrodes into primary visual cortex (V1) of rats, we conducted extracellular recordings of single units and followed the same cell ensembles in the awake and anesthetized states. We found that the transition from wakefulness to anesthesia involves unpredictable changes in temporal response characteristics. The latency of single-unit responses to visual stimulation was delayed in anesthesia, with large individual variations between units. Pair-wise correlations between units increased under anesthesia, indicating more synchronized activity. Further, the units within an ensemble show reproducible temporal activity patterns in response to visual stimuli that is changed between states, suggesting state-dependent sequences of activity. The current dataset, with recordings from the same neural ensembles across states, is well suited for validating and testing computational network models. This can lead to testable predictions, bring a deeper understanding of the experimental findings and improve models of neural information processing. Here, we exemplify such a workflow using a Brunel network model. PMID:28791331
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NASA Astrophysics Data System (ADS)
Hilbert, Stefan; Dunkel, Jörn
2006-07-01
We calculate exactly both the microcanonical and canonical thermodynamic functions (TDFs) for a one-dimensional model system with piecewise constant Lennard-Jones type pair interactions. In the case of an isolated N -particle system, the microcanonical TDFs exhibit (N-1) singular (nonanalytic) microscopic phase transitions of the formal order N/2 , separating N energetically different evaporation (dissociation) states. In a suitably designed evaporation experiment, these types of phase transitions should manifest themselves in the form of pressure and temperature oscillations, indicating cooling by evaporation. In the presence of a heat bath (thermostat), such oscillations are absent, but the canonical heat capacity shows a characteristic peak, indicating the temperature-induced dissociation of the one-dimensional chain. The distribution of complex zeros of the canonical partition may be used to identify different degrees of dissociation in the canonical ensemble.
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NASA Astrophysics Data System (ADS)
Csordás, A.; Graham, R.; Szépfalusy, P.; Vattay, G.
1994-01-01
One wall of an Artin's billiard on the Poincaré half-plane is replaced by a one-parameter (cp) family of nongeodetic walls. A brief description of the classical phase space of this system is given. In the quantum domain, the continuous and gradual transition from the Poisson-like to Gaussian-orthogonal-ensemble (GOE) level statistics due to the small perturbations breaking the symmetry responsible for the ``arithmetic chaos'' at cp=1 is studied. Another GOE-->Poisson transition due to the mixed phase space for large perturbations is also investigated. A satisfactory description of the intermediate level statistics by the Brody distribution was found in both cases. The study supports the existence of a scaling region around cp=1. A finite-size scaling relation for the Brody parameter as a function of 1-cp and the number of levels considered can be established.
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Oliveira, Roberta B; Pereira, Aledir S; Tavares, João Manuel R S
2017-10-01
The number of deaths worldwide due to melanoma has risen in recent times, in part because melanoma is the most aggressive type of skin cancer. Computational systems have been developed to assist dermatologists in early diagnosis of skin cancer, or even to monitor skin lesions. However, there still remains a challenge to improve classifiers for the diagnosis of such skin lesions. The main objective of this article is to evaluate different ensemble classification models based on input feature manipulation to diagnose skin lesions. Input feature manipulation processes are based on feature subset selections from shape properties, colour variation and texture analysis to generate diversity for the ensemble models. Three subset selection models are presented here: (1) a subset selection model based on specific feature groups, (2) a correlation-based subset selection model, and (3) a subset selection model based on feature selection algorithms. Each ensemble classification model is generated using an optimum-path forest classifier and integrated with a majority voting strategy. The proposed models were applied on a set of 1104 dermoscopic images using a cross-validation procedure. The best results were obtained by the first ensemble classification model that generates a feature subset ensemble based on specific feature groups. The skin lesion diagnosis computational system achieved 94.3% accuracy, 91.8% sensitivity and 96.7% specificity. The input feature manipulation process based on specific feature subsets generated the greatest diversity for the ensemble classification model with very promising results. Copyright © 2017 Elsevier B.V. All rights reserved.
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ERIC Educational Resources Information Center
1999
This document contains four symposium papers on work force development. "Effects of Two Different Learning Paths on School-to-Work Transition" (Esther Van Der Schoot) discusses a Dutch study documenting that the following items make a difference in the school-to-work transition: learning path, curriculum characteristics, individual…
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Method of inducing surface ensembles on a metal catalyst
Miller, Steven S.
1989-01-01
A method of inducing surface ensembles on a transition metal catalyst used in the conversion of a reactant gas or gas mixture, such as carbon monoxide and hydrogen into hydrocarbons (the Fischer-Tropsch reaction) is disclosed which comprises adding a Lewis base to the syngas (CO+H.sub.2) mixture before reaction takes place. The formation of surface ensembles in this manner restricts the number and types of reaction pathways which will be utilized, thus greatly narrowing the product distribution and maximizing the efficiency of the Fischer-Tropsch reaction. Similarly, amines may also be produced by the conversion of reactant gas or gases, such as nitrogen, hydrogen, or hydrocarbon constituents.
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Method of inducing surface ensembles on a metal catalyst
Miller, S.S.
1987-10-02
A method of inducing surface ensembles on a transition metal catalyst used in the conversion of a reactant gas or gas mixture, such as carbon monoxide and hydrogen into hydrocarbons (the Fischer-Tropsch reaction) is disclosed which comprises adding a Lewis base to the syngas (CO + H/sub 2/) mixture before reaction takes place. The formation of surface ensembles in this manner restricts the number and types of reaction pathways which will be utilized, thus greatly narrowing the product distribution and maximizing the efficiency of the Fischer-Tropsch reaction. Similarly, amines may also be produced by the conversion of reactant gas or gases, such as nitrogen, hydrogen, or hydrocarbon constituents.
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Liu, Zhao; Zhu, Yunhong; Wu, Chenxue
2016-01-01
Spatial-temporal k-anonymity has become a mainstream approach among techniques for protection of users’ privacy in location-based services (LBS) applications, and has been applied to several variants such as LBS snapshot queries and continuous queries. Analyzing large-scale spatial-temporal anonymity sets may benefit several LBS applications. In this paper, we propose two location prediction methods based on transition probability matrices constructing from sequential rules for spatial-temporal k-anonymity dataset. First, we define single-step sequential rules mined from sequential spatial-temporal k-anonymity datasets generated from continuous LBS queries for multiple users. We then construct transition probability matrices from mined single-step sequential rules, and normalize the transition probabilities in the transition matrices. Next, we regard a mobility model for an LBS requester as a stationary stochastic process and compute the n-step transition probability matrices by raising the normalized transition probability matrices to the power n. Furthermore, we propose two location prediction methods: rough prediction and accurate prediction. The former achieves the probabilities of arriving at target locations along simple paths those include only current locations, target locations and transition steps. By iteratively combining the probabilities for simple paths with n steps and the probabilities for detailed paths with n-1 steps, the latter method calculates transition probabilities for detailed paths with n steps from current locations to target locations. Finally, we conduct extensive experiments, and correctness and flexibility of our proposed algorithm have been verified. PMID:27508502
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Lu, Qing; Kim, Jaegil; Straub, John E
2013-03-14
The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.
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Use of combined radar and radiometer systems in space for precipitation measurement: Some ideas
NASA Technical Reports Server (NTRS)
Moore, R. K.
1981-01-01
A brief survey is given of some fundamental physical concepts of optimal polarization characteristics of a transmission path or scatter ensemble of hydrometers. It is argued that, based on this optimization concept, definite advances in remote atmospheric sensing are to be expected. Basic properties of Kennaugh's optimal polarization theory are identified.
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Observation of ground-state quantum beats in atomic spontaneous emission.
Norris, D G; Orozco, L A; Barberis-Blostein, P; Carmichael, H J
2010-09-17
We report ground-state quantum beats in spontaneous emission from a continuously driven atomic ensemble. Beats are visible only in an intensity autocorrelation and evidence spontaneously generated coherence in radiative decay. Our measurement realizes a quantum eraser where a first photon detection prepares a superposition and a second erases the "which path" information in the intermediate state.
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Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu
2008-01-01
A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.
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Jia, Chen
2017-09-01
Here we develop an effective approach to simplify two-time-scale Markov chains with infinite state spaces by removal of states with fast leaving rates, which improves the simplification method of finite Markov chains. We introduce the concept of fast transition paths and show that the effective transitions of the reduced chain can be represented as the superposition of the direct transitions and the indirect transitions via all the fast transition paths. Furthermore, we apply our simplification approach to the standard Markov model of single-cell stochastic gene expression and provide a mathematical theory of random gene expression bursts. We give the precise mathematical conditions for the bursting kinetics of both mRNAs and proteins. It turns out that random bursts exactly correspond to the fast transition paths of the Markov model. This helps us gain a better understanding of the physics behind the bursting kinetics as an emergent behavior from the fundamental multiscale biochemical reaction kinetics of stochastic gene expression.
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NASA Astrophysics Data System (ADS)
Jia, Chen
2017-09-01
Here we develop an effective approach to simplify two-time-scale Markov chains with infinite state spaces by removal of states with fast leaving rates, which improves the simplification method of finite Markov chains. We introduce the concept of fast transition paths and show that the effective transitions of the reduced chain can be represented as the superposition of the direct transitions and the indirect transitions via all the fast transition paths. Furthermore, we apply our simplification approach to the standard Markov model of single-cell stochastic gene expression and provide a mathematical theory of random gene expression bursts. We give the precise mathematical conditions for the bursting kinetics of both mRNAs and proteins. It turns out that random bursts exactly correspond to the fast transition paths of the Markov model. This helps us gain a better understanding of the physics behind the bursting kinetics as an emergent behavior from the fundamental multiscale biochemical reaction kinetics of stochastic gene expression.
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Transition of recollision trajectories from linear to elliptical polarization
Li, Yingbin; Yu, Benhai; Tang, Qingbin; ...
2016-03-15
Using a classical ensemble method, we revisit the topic of recollision and nonsequential double ionization with elliptically polarized laser fields. We focus on how the recollision mechanism transitions from short trajectories with linear polarization to long trajectories with elliptical polarization. Furthermore, we propose how this transition can be observed by measuring the carrier-envelop-phase dependence of the correlated electron momentum spectra using currently available few-cycle laser pulses.
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Neural Representation of Spatial Topology in the Rodent Hippocampus
Chen, Zhe; Gomperts, Stephen N.; Yamamoto, Jun; Wilson, Matthew A.
2014-01-01
Pyramidal cells in the rodent hippocampus often exhibit clear spatial tuning in navigation. Although it has been long suggested that pyramidal cell activity may underlie a topological code rather than a topographic code, it remains unclear whether an abstract spatial topology can be encoded in the ensemble spiking activity of hippocampal place cells. Using a statistical approach developed previously, we investigate this question and related issues in greater details. We recorded ensembles of hippocampal neurons as rodents freely foraged in one and two-dimensional spatial environments, and we used a “decode-to-uncover” strategy to examine the temporally structured patterns embedded in the ensemble spiking activity in the absence of observed spatial correlates during periods of rodent navigation or awake immobility. Specifically, the spatial environment was represented by a finite discrete state space. Trajectories across spatial locations (“states”) were associated with consistent hippocampal ensemble spiking patterns, which were characterized by a state transition matrix. From this state transition matrix, we inferred a topology graph that defined the connectivity in the state space. In both one and two-dimensional environments, the extracted behavior patterns from the rodent hippocampal population codes were compared against randomly shuffled spike data. In contrast to a topographic code, our results support the efficiency of topological coding in the presence of sparse sample size and fuzzy space mapping. This computational approach allows us to quantify the variability of ensemble spiking activity, to examine hippocampal population codes during off-line states, and to quantify the topological complexity of the environment. PMID:24102128
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NASA Astrophysics Data System (ADS)
Li, Hui-Ling; Feng, Zhong-Wen; Zu, Xiao-Tao
2018-01-01
With motivation by holography, employing black hole entropy, two-point connection function and entanglement entropy, we show that, for the higher-dimensional Anti-de Sitter charged hairy black hole in the fixed charged ensemble, a Van der Waals-like phase transition can be observed. Furthermore, based on the Maxwell equal-area construction, we check numerically the equal-area law for a first order phase transition in order to further characterize the Van der Waals-like phase transition.
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Ensemble Modeling of the July 23, 2012 CME Event
NASA Astrophysics Data System (ADS)
Cash, M. D.; Biesecker, D. A.; Millward, G.; Arge, C. N.; Henney, C. J.
2013-12-01
On July 23, 2012 a large and very fast coronal mass ejection (CME) was observed by STEREO A. This CME was unusual in that the estimates of the speed of the CME ranged from 2125 km/s to 2780 km/s based on dividing the distance of STEREO A from the Sun by the transit time of the CME. Modeling of this CME event with the WSA-Enlil model has also suggested that a very fast speed is required in order to obtain the correct arrival time at 1 AU. We present a systematic study of parameter space for the July 23, 2012 CME event through an ensemble study using the WSA-Enlil model to predict the arrival time of the CME at STEREO A. We investigate how variations in the initial speed, angular width, and direction affect the predicted arrival time. We also explore how variations in the background solar wind influence CME arrival time by using varying ADAPT maps within our ensemble study. Factors involved in the fast transit time of this large CME are discussed and the optimal CME parameters are presented.
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Inhomogeneous diffusion and ergodicity breaking induced by global memory effects
NASA Astrophysics Data System (ADS)
Budini, Adrián A.
2016-11-01
We introduce a class of discrete random-walk model driven by global memory effects. At any time, the right-left transitions depend on the whole previous history of the walker, being defined by an urnlike memory mechanism. The characteristic function is calculated in an exact way, which allows us to demonstrate that the ensemble of realizations is ballistic. Asymptotically, each realization is equivalent to that of a biased Markovian diffusion process with transition rates that strongly differs from one trajectory to another. Using this "inhomogeneous diffusion" feature, the ergodic properties of the dynamics are analytically studied through the time-averaged moments. Even in the long-time regime, they remain random objects. While their average over realizations recovers the corresponding ensemble averages, departure between time and ensemble averages is explicitly shown through their probability densities. For the density of the second time-averaged moment, an ergodic limit and the limit of infinite lag times do not commutate. All these effects are induced by the memory effects. A generalized Einstein fluctuation-dissipation relation is also obtained for the time-averaged moments.
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All-optical coherent population trapping with defect spin ensembles in silicon carbide.
Zwier, Olger V; O'Shea, Danny; Onur, Alexander R; van der Wal, Caspar H
2015-06-05
Divacancy defects in silicon carbide have long-lived electronic spin states and sharp optical transitions. Because of the various polytypes of SiC, hundreds of unique divacancies exist, many with spin properties comparable to the nitrogen-vacancy center in diamond. If ensembles of such spins can be all-optically manipulated, they make compelling candidate systems for quantum-enhanced memory, communication, and sensing applications. We report here direct all-optical addressing of basal plane-oriented divacancy spins in 4H-SiC. By means of magneto-spectroscopy, we fully identify the spin triplet structure of both the ground and the excited state, and use this for tuning of transition dipole moments between particular spin levels. We also identify a role for relaxation via intersystem crossing. Building on these results, we demonstrate coherent population trapping -a key effect for quantum state transfer between spins and photons- for divacancy sub-ensembles along particular crystal axes. These results, combined with the flexibility of SiC polytypes and device processing, put SiC at the forefront of quantum information science in the solid state.
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NASA Astrophysics Data System (ADS)
O'Brien, Edward; Vendruscolo, Michele; Dobson, Christopher
2010-03-01
In vitro experiments examining cotranslational folding utilize ribosome-nascent chain complexes (RNCs) in which the nascent chain is stalled at different points of its biosynthesis on the ribosome. We investigate the thermodynamics, kinetics, and structural properties of RNCs containing five different globular and repeat proteins stalled at ten different nascent chain lengths using coarse grained replica exchange simulations. We find that when the proteins are stalled near the ribosome exit tunnel opening they exhibit altered folding coopserativity, quantified by the van't Hoff enthalpy criterion; a significantly altered denatured state ensemble, in terms of Rg and shape parameters (Rg tensor); and the appearance of partially folded intermediates during cotranslation, evidenced by the appearance of a third basin in the free energy profile. These trends are due in part to excluded volume (crowding) interactions between the ribosome and nascent chain. We perform in silico temperature-jump experiments on the RNCs and examine nascent chain folding kinetics and structural changes in the transition state ensemble at various stall lengths.
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NASA Astrophysics Data System (ADS)
Matsunaga, Y.; Sugita, Y.
2018-06-01
A data-driven modeling scheme is proposed for conformational dynamics of biomolecules based on molecular dynamics (MD) simulations and experimental measurements. In this scheme, an initial Markov State Model (MSM) is constructed from MD simulation trajectories, and then, the MSM parameters are refined using experimental measurements through machine learning techniques. The second step can reduce the bias of MD simulation results due to inaccurate force-field parameters. Either time-series trajectories or ensemble-averaged data are available as a training data set in the scheme. Using a coarse-grained model of a dye-labeled polyproline-20, we compare the performance of machine learning estimations from the two types of training data sets. Machine learning from time-series data could provide the equilibrium populations of conformational states as well as their transition probabilities. It estimates hidden conformational states in more robust ways compared to that from ensemble-averaged data although there are limitations in estimating the transition probabilities between minor states. We discuss how to use the machine learning scheme for various experimental measurements including single-molecule time-series trajectories.
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A new large initial condition ensemble to assess avoided impacts in a climate mitigation scenario
NASA Astrophysics Data System (ADS)
Sanderson, B. M.; Tebaldi, C.; Knutti, R.; Oleson, K. W.
2014-12-01
It has recently been demonstrated that when considering timescales of up to 50 years, natural variability may play an equal role to anthropogenic forcing on subcontinental trends for a variety of climate indicators. Thus, for many questions assessing climate impacts on such time and spatial scales, it has become clear that a significant number of ensemble members may be required to produce robust statistics (and especially so for extreme events). However, large ensemble experiments to date have considered the role of variability in a single scenario, leaving uncertain the relationship between the forced climate trajectory and the variability about that path. To address this issue, we present a new, publicly available, 15 member initial condition ensemble of 21st century climate projections for the RCP 4.5 scenario using the CESM1.1 Earth System Model, which we propose as a companion project to the existing 40 member CESM large ensemble which uses the higher greenhouse gas emission future of RCP8.5. This provides a valuable data set for assessing what societal and ecological impacts might be avoided through a moderate mitigation strategy in contrast to a fossil fuel intensive future. We present some early analyses of these combined ensembles to assess to what degree the climate variability can be considered to combine linearly with the underlying forced response. In regions where there is no detectable relationship between the mean state and the variability about the mean trajectory, then linear assumptions can be trivially exploited to utilize a single ensemble or control simulation to characterize the variability in any scenario of interest. We highlight regions where there is a detectable nonlinearity in extreme event frequency, how far in the future they will be manifested and propose mechanisms to account for these effects.
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Liu, Lei; Cao, Zanxia
2013-01-01
The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH. PMID:23708094
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NASA Astrophysics Data System (ADS)
Livorati, André L. P.; Palmero, Matheus S.; Díaz-I, Gabriel; Dettmann, Carl P.; Caldas, Iberê L.; Leonel, Edson D.
2018-02-01
We study the dynamics of an ensemble of non interacting particles constrained by two infinitely heavy walls, where one of them is moving periodically in time, while the other is fixed. The system presents mixed dynamics, where the accessible region for the particle to diffuse chaotically is bordered by an invariant spanning curve. Statistical analysis for the root mean square velocity, considering high and low velocity ensembles, leads the dynamics to the same steady state plateau for long times. A transport investigation of the dynamics via escape basins reveals that depending of the initial velocity ensemble, the decay rates of the survival probability present different shapes and bumps, in a mix of exponential, power law and stretched exponential decays. After an analysis of step-size averages, we found that the stable manifolds play the role of a preferential path for faster escape, being responsible for the bumps and different shapes of the survival probability.
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Crossover ensembles of random matrices and skew-orthogonal polynomials
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kumar, Santosh, E-mail: skumar.physics@gmail.com; Pandey, Akhilesh, E-mail: ap0700@mail.jnu.ac.in
2011-08-15
Highlights: > We study crossover ensembles of Jacobi family of random matrices. > We consider correlations for orthogonal-unitary and symplectic-unitary crossovers. > We use the method of skew-orthogonal polynomials and quaternion determinants. > We prove universality of spectral correlations in crossover ensembles. > We discuss applications to quantum conductance and communication theory problems. - Abstract: In a recent paper (S. Kumar, A. Pandey, Phys. Rev. E, 79, 2009, p. 026211) we considered Jacobi family (including Laguerre and Gaussian cases) of random matrix ensembles and reported exact solutions of crossover problems involving time-reversal symmetry breaking. In the present paper we givemore » details of the work. We start with Dyson's Brownian motion description of random matrix ensembles and obtain universal hierarchic relations among the unfolded correlation functions. For arbitrary dimensions we derive the joint probability density (jpd) of eigenvalues for all transitions leading to unitary ensembles as equilibrium ensembles. We focus on the orthogonal-unitary and symplectic-unitary crossovers and give generic expressions for jpd of eigenvalues, two-point kernels and n-level correlation functions. This involves generalization of the theory of skew-orthogonal polynomials to crossover ensembles. We also consider crossovers in the circular ensembles to show the generality of our method. In the large dimensionality limit, correlations in spectra with arbitrary initial density are shown to be universal when expressed in terms of a rescaled symmetry breaking parameter. Applications of our crossover results to communication theory and quantum conductance problems are also briefly discussed.« less
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Parameter Uncertainty on AGCM-simulated Tropical Cyclones
NASA Astrophysics Data System (ADS)
He, F.
2015-12-01
This work studies the parameter uncertainty on tropical cyclone (TC) simulations in Atmospheric General Circulation Models (AGCMs) using the Reed-Jablonowski TC test case, which is illustrated in Community Atmosphere Model (CAM). It examines the impact from 24 parameters across the physical parameterization schemes that represent the convection, turbulence, precipitation and cloud processes in AGCMs. The one-at-a-time (OAT) sensitivity analysis method first quantifies their relative importance on TC simulations and identifies the key parameters to the six different TC characteristics: intensity, precipitation, longwave cloud radiative forcing (LWCF), shortwave cloud radiative forcing (SWCF), cloud liquid water path (LWP) and ice water path (IWP). Then, 8 physical parameters are chosen and perturbed using the Latin-Hypercube Sampling (LHS) method. The comparison between OAT ensemble run and LHS ensemble run shows that the simulated TC intensity is mainly affected by the parcel fractional mass entrainment rate in Zhang-McFarlane (ZM) deep convection scheme. The nonlinear interactive effect among different physical parameters is negligible on simulated TC intensity. In contrast, this nonlinear interactive effect plays a significant role in other simulated tropical cyclone characteristics (precipitation, LWCF, SWCF, LWP and IWP) and greatly enlarge their simulated uncertainties. The statistical emulator Extended Multivariate Adaptive Regression Splines (EMARS) is applied to characterize the response functions for nonlinear effect. Last, we find that the intensity uncertainty caused by physical parameters is in a degree comparable to uncertainty caused by model structure (e.g. grid) and initial conditions (e.g. sea surface temperature, atmospheric moisture). These findings suggest the importance of using the perturbed physics ensemble (PPE) method to revisit tropical cyclone prediction under climate change scenario.
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Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy
NASA Astrophysics Data System (ADS)
Minh, David D. L.; Adib, Artur B.
2008-05-01
An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.
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Spectral partitioning in equitable graphs.
Barucca, Paolo
2017-06-01
Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.
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Spectral partitioning in equitable graphs
NASA Astrophysics Data System (ADS)
Barucca, Paolo
2017-06-01
Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.
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Double-well chimeras in 2D lattice of chaotic bistable elements
NASA Astrophysics Data System (ADS)
Shepelev, I. A.; Bukh, A. V.; Vadivasova, T. E.; Anishchenko, V. S.; Zakharova, A.
2018-01-01
We investigate spatio-temporal dynamics of a 2D ensemble of nonlocally coupled chaotic cubic maps in a bistability regime. In particular, we perform a detailed study on the transition ;coherence - incoherence; for varying coupling strength for a fixed interaction radius. For the 2D ensemble we show the appearance of amplitude and phase chimera states previously reported for 1D ensembles of nonlocally coupled chaotic systems. Moreover, we uncover a novel type of chimera state, double-well chimera, which occurs due to the interplay of the bistability of the local dynamics and the 2D ensemble structure. Additionally, we find double-well chimera behavior for steady states which we call double-well chimera death. A distinguishing feature of chimera patterns observed in the lattice is that they mainly combine clusters of different chimera types: phase, amplitude and double-well chimeras.
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Coherent Magnetic Response at Optical Frequencies Using Atomic Transitions
NASA Astrophysics Data System (ADS)
Brewer, Nicholas R.; Buckholtz, Zachary N.; Simmons, Zachary J.; Mueller, Eli A.; Yavuz, Deniz D.
2017-01-01
In optics, the interaction of atoms with the magnetic field of light is almost always ignored since its strength is many orders of magnitude weaker compared to the interaction with the electric field. In this article, by using a magnetic-dipole transition within the 4 f shell of europium ions, we show a strong interaction between a green laser and an ensemble of atomic ions. The electrons move coherently between the ground and excited ionic levels (Rabi flopping) by interacting with the magnetic field of the laser. By measuring the Rabi flopping frequency as the laser intensity is varied, we report the first direct measurement of a magnetic-dipole matrix element in the optical region of the spectrum. Using density-matrix simulations of the ensemble, we infer the generation of coherent magnetization with magnitude 5.5 ×10-3 A /m , which is capable of generating left-handed electromagnetic waves of intensity 1 nW /cm2 . These results open up the prospect of constructing left-handed materials using sharp transitions of atoms.
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Transition to collective oscillations in finite Kuramoto ensembles
NASA Astrophysics Data System (ADS)
Peter, Franziska; Pikovsky, Arkady
2018-03-01
We present an alternative approach to finite-size effects around the synchronization transition in the standard Kuramoto model. Our main focus lies on the conditions under which a collective oscillatory mode is well defined. For this purpose, the minimal value of the amplitude of the complex Kuramoto order parameter appears as a proper indicator. The dependence of this minimum on coupling strength varies due to sampling variations and correlates with the sample kurtosis of the natural frequency distribution. The skewness of the frequency sample determines the frequency of the resulting collective mode. The effects of kurtosis and skewness hold in the thermodynamic limit of infinite ensembles. We prove this by integrating a self-consistency equation for the complex Kuramoto order parameter for two families of distributions with controlled kurtosis and skewness, respectively.
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Drift-Induced Selection Between Male and Female Heterogamety.
Veller, Carl; Muralidhar, Pavitra; Constable, George W A; Nowak, Martin A
2017-10-01
Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of "drift-induced selection" operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems. Copyright © 2017 by the Genetics Society of America.
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NASA Technical Reports Server (NTRS)
2011-01-01
NASA is interested in developing technology that leads to more routine, safe, and affordable access to space. Access to space using airbreathing propulsion systems has potential to meet these objectives based on Airbreathing Access to Space (AAS) system studies. To this end, the NASA Fundamental Aeronautics Program (FAP) Hypersonic Project is conducting fundamental research on a Turbine Based Combined Cycle (TBCC) propulsion system. The TBCC being studied considers a dual flow-path inlet system. One flow-path includes variable geometry to regulate airflow to a turbine engine cycle. The turbine cycle provides propulsion from take-off to supersonic flight. The second flow-path supports a dual-mode scramjet (DMSJ) cycle which would be initiated at supersonic speed to further accelerate the vehicle to hypersonic speed. For a TBCC propulsion system to accelerate a vehicle from supersonic to hypersonic speed, a critical enabling technology is the ability to safely and effectively transition from the turbine to the DMSJ-referred to as mode transition. To experimentally test methods of mode transition, a Combined Cycle Engine (CCE) Large-scale Inlet testbed was designed with two flow paths-a low speed flow-path sized for a turbine cycle and a high speed flow-path designed for a DMSJ. This testbed system is identified as the CCE Large-Scale Inlet for Mode Transition studies (CCE-LIMX). The test plan for the CCE-LIMX in the NASA Glenn Research Center (GRC) 10- by 10-ft Supersonic Wind Tunnel (10x10 SWT) is segmented into multiple phases. The first phase is a matrix of inlet characterization (IC) tests to evaluate the inlet performance and establish the mode transition schedule. The second phase is a matrix of dynamic system identification (SysID) experiments designed to support closed-loop control development at mode transition schedule operating points for the CCE-LIMX. The third phase includes a direct demonstration of controlled mode transition using a closed loop control system developed with the data obtained from the first two phases. Plans for a fourth phase include mode transition experiments with a turbine engine. This paper, focusing on the first two phases of experiments, presents developed operational and analysis tools for streamlined testing and data reduction procedures.
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California PATH : 1997 annual report
DOT National Transportation Integrated Search
1997-01-01
The California Partners for Advanced Transit and Highways Program (PATH) has been leading the way in ITS (Intelligent Transportation Systems) research since PATHs founding in 1986, before the term ITS or its predecessor IVHS (Intelligent Vehicle H...
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California PATH : 1996 annual report
DOT National Transportation Integrated Search
1996-01-01
The California Partners for Advanced Transit and Highways Program (PATH ) has been leading the way in ITS (Intelligent Transportation Systems) research since PATH's founding in 1986, before the term ITS or its predecessor IVHS (Intelligent Vehicle Hi...
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Nonequilibrium Phase Transitions in Supercooled Water
NASA Astrophysics Data System (ADS)
Limmer, David; Chandler, David
2012-02-01
We present results of a simulation study of water driven out of equilibrium. Using transition path sampling, we can probe stationary path distributions parameterize by order parameters that are extensive in space and time. We find that by coupling external fields to these parameters, we can drive water through a first order dynamical phase transition into amorphous ice. By varying the initial equilibrium distributions we can probe pathways for the creation of amorphous ices of low and high densities.
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NASA Astrophysics Data System (ADS)
Zuehlsdorff, T. J.; Isborn, C. M.
2018-01-01
The correct treatment of vibronic effects is vital for the modeling of absorption spectra of many solvated dyes. Vibronic spectra for small dyes in solution can be easily computed within the Franck-Condon approximation using an implicit solvent model. However, implicit solvent models neglect specific solute-solvent interactions on the electronic excited state. On the other hand, a straightforward way to account for solute-solvent interactions and temperature-dependent broadening is by computing vertical excitation energies obtained from an ensemble of solute-solvent conformations. Ensemble approaches usually do not account for vibronic transitions and thus often produce spectral shapes in poor agreement with experiment. We address these shortcomings by combining zero-temperature vibronic fine structure with vertical excitations computed for a room-temperature ensemble of solute-solvent configurations. In this combined approach, all temperature-dependent broadening is treated classically through the sampling of configurations and quantum mechanical vibronic contributions are included as a zero-temperature correction to each vertical transition. In our calculation of the vertical excitations, significant regions of the solvent environment are treated fully quantum mechanically to account for solute-solvent polarization and charge-transfer. For the Franck-Condon calculations, a small amount of frozen explicit solvent is considered in order to capture solvent effects on the vibronic shape function. We test the proposed method by comparing calculated and experimental absorption spectra of Nile red and the green fluorescent protein chromophore in polar and non-polar solvents. For systems with strong solute-solvent interactions, the combined approach yields significant improvements over the ensemble approach. For systems with weak to moderate solute-solvent interactions, both the high-energy vibronic tail and the width of the spectra are in excellent agreement with experiments.
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Predictor laws for pictorial flight displays
NASA Technical Reports Server (NTRS)
Grunwald, A. J.
1985-01-01
Two predictor laws are formulated and analyzed: (1) a circular path law based on constant accelerations perpendicular to the path and (2) a predictor law based on state transition matrix computations. It is shown that for both methods the predictor provides the essential lead zeros for the path-following task. However, in contrast to the circular path law, the state transition matrix law furnishes the system with additional zeros that entirely cancel out the higher-frequency poles of the vehicle dynamics. On the other hand, the circular path law yields a zero steady-state error in following a curved trajectory with a constant radius. A combined predictor law is suggested that utilizes the advantages of both methods. A simple analysis shows that the optimal prediction time mainly depends on the level of precision required in the path-following task, and guidelines for determining the optimal prediction time are given.
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Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.
Maximova, Tatiana; Plaku, Erion; Shehu, Amarda
2016-07-07
Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.
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NASA Astrophysics Data System (ADS)
Li, J. F.; Waliser, D. E.; Chen, W.; Deng, M.; Lebsock, M. D.; Stephens, G. L.; Guan, B.; Christensen, M.; Teixeira, J.
2013-12-01
Representing clouds and cloud climate feedbacks in global climate models (GCMs) remains a pressing challenge to reduce and quantify uncertainties associated with climate change projection. Vertical structures of clouds simulated by present-day models have not been extensively examined using vertically-resolved cloud hydrometers such as cloud ice water (CIW) content and cloud liquid water (CLW) content. The gap in available observations for cloud mass was clearly evident from the wide disparity in the CIW path [Waliser et al., 2009] and CLW path [Li et al., 2008;2011] values exhibited in the CMIP3 GCMs. We present an observationally-based evaluation of the CIW and CLW of present-day GCMs, notably 20th century CMIP5 simulations, and compare these results to the CMIP3 and two recent reanalyses (ECMWF and MERRA). We use three different CloudSat+CALIPSO CIW products as well as three different observation CLW products, CloudSat, MODIS and AMSRE and their combined product for CLW with methods to remove the contribution from the convective core ice mass and/or precipitating cloud hydrometeors with variable sizes and falling speeds so that a robust observational estimate with uncertainty can be obtained for model evaluations. Note, considering the CloudSat's limitations of CLW retrievals due to contamination from the precipitation and from radar clutter near the surface, an alternative CLW is synergistically constructed using MODIS CLW and CloudSat CLW. The results show that for annual mean CIW path, there are factors of 2-10 in the differences between observations and models for a majority of the GCMs and for a number of regions. Based on a number of metrics, the ensemble behavior of CMIP5 has improved considerably relative to CMIP3 (~ 50%), although neither the CMIP5 ensemble mean nor any individual model performs particularly well, and there are still a number of models that exhibit very large biases despite the availability of relevant observations. For CLW, most of the CMIP3/CMIP5 annual mean CLW path values are overestimated by factors of 2-10 compared to observations globally. For the vertical structure of CIW/CLW content, significant systematic biases are found with many models biased significantly. Based on the Taylor diagram, the ensemble performance of CMIP5 CLW path simulation shows little or no improvement relative to CMIP3. The implications of these results on model representations of the earth radiation balance are discussed, along with caveats and uncertainties associated with the observational estimates, model and observation representations of the precipitating and cloudy ice components, relevant physical processes and parameterizations.
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NASA Astrophysics Data System (ADS)
Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher
2014-01-01
We have developed a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. In this paper, we set the theoretical framework for employing nonequilibrium work relations to estimate the relative reaction rates associated with different classes of transition pathways. Particularly, we derive an extension of Crook's transient fluctuation theorem, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements (e.g., in Steered Molecular Dynamics). The formalism presented here can be combined with Transition Path Theory to relate the equilibrium and driven transition rates. The usefulness of this framework is illustrated by means of a Gaussian model and a driven proline dimer.
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McMahan, Kevin Weston; Dillard, Daniel Jackson
2016-05-03
A turbine system is disclosed. The turbine system includes a transition duct having an inlet, an outlet, and a passage extending between the inlet and the outlet and defining a longitudinal axis, a radial axis, and a tangential axis. The outlet of the transition duct is offset from the inlet along the longitudinal axis and the tangential axis. The turbine system further includes a turbine section connected to the transition duct. The turbine section includes a plurality of shroud blocks at least partially defining a hot gas path, a plurality of buckets at least partially disposed in the hot gas path, and a plurality of nozzles at least partially disposed in the hot gas path. At least one of a shroud block, a bucket, or a nozzle includes means for withstanding high temperatures.
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Robust techniques for polarization and detection of nuclear spin ensembles
NASA Astrophysics Data System (ADS)
Scheuer, Jochen; Schwartz, Ilai; Müller, Samuel; Chen, Qiong; Dhand, Ish; Plenio, Martin B.; Naydenov, Boris; Jelezko, Fedor
2017-11-01
Highly sensitive nuclear spin detection is crucial in many scientific areas including nuclear magnetic resonance spectroscopy, magnetic resonance imaging (MRI), and quantum computing. The tiny thermal nuclear spin polarization represents a major obstacle towards this goal which may be overcome by dynamic nuclear spin polarization (DNP) methods. The latter often rely on the transfer of the thermally polarized electron spins to nearby nuclear spins, which is limited by the Boltzmann distribution of the former. Here we utilize microwave dressed states to transfer the high (>92 % ) nonequilibrium electron spin polarization of a single nitrogen-vacancy center (NV) induced by short laser pulses to the surrounding 13C carbon nuclear spins. The NV is repeatedly repolarized optically, thus providing an effectively infinite polarization reservoir. A saturation of the polarization of the nearby nuclear spins is achieved, which is confirmed by the decay of the polarization transfer signal and shows an excellent agreement with theoretical simulations. Hereby we introduce the polarization readout by polarization inversion method as a quantitative magnetization measure of the nuclear spin bath, which allows us to observe by ensemble averaging macroscopically hidden polarization dynamics like Landau-Zener-Stückelberg oscillations. Moreover, we show that using the integrated solid effect both for single- and double-quantum transitions nuclear spin polarization can be achieved even when the static magnetic field is not aligned along the NV's crystal axis. This opens a path for the application of our DNP technique to spins in and outside of nanodiamonds, enabling their application as MRI tracers. Furthermore, the methods reported here can be applied to other solid state systems where a central electron spin is coupled to a nuclear spin bath, e.g., phosphor donors in silicon and color centers in silicon carbide.
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A path-integral approach to the problem of time
NASA Astrophysics Data System (ADS)
Amaral, M. M.; Bojowald, Martin
2018-01-01
Quantum transition amplitudes are formulated for model systems with local internal time, using intuition from path integrals. The amplitudes are shown to be more regular near a turning point of internal time than could be expected based on existing canonical treatments. In particular, a successful transition through a turning point is provided in the model systems, together with a new definition of such a transition in general terms. Some of the results rely on a fruitful relation between the problem of time and general Gribov problems.
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Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States
NASA Astrophysics Data System (ADS)
de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M.
2018-03-01
Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.
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Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.
de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M
2018-03-23
Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.
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The integrated process rates (IPR) estimated by the Eta-CMAQ model at grid cells along the trajectory of the air mass transport path were analyzed to quantitatively investigate the relative importance of physical and chemical processes for O3 formation and evolution ov...
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On the use of transition matrix methods with extended ensembles.
Escobedo, Fernando A; Abreu, Charlles R A
2006-03-14
Different extended ensemble schemes for non-Boltzmann sampling (NBS) of a selected reaction coordinate lambda were formulated so that they employ (i) "variable" sampling window schemes (that include the "successive umbrella sampling" method) to comprehensibly explore the lambda domain and (ii) transition matrix methods to iteratively obtain the underlying free-energy eta landscape (or "importance" weights) associated with lambda. The connection between "acceptance ratio" and transition matrix methods was first established to form the basis of the approach for estimating eta(lambda). The validity and performance of the different NBS schemes were then assessed using as lambda coordinate the configurational energy of the Lennard-Jones fluid. For the cases studied, it was found that the convergence rate in the estimation of eta is little affected by the use of data from high-order transitions, while it is noticeably improved by the use of a broader window of sampling in the variable window methods. Finally, it is shown how an "elastic" window of sampling can be used to effectively enact (nonuniform) preferential sampling over the lambda domain, and how to stitch the weights from separate one-dimensional NBS runs to produce a eta surface over a two-dimensional domain.
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Vyas, Manan; Kota, V K B; Chavda, N D
2010-03-01
Finite interacting Fermi systems with a mean-field and a chaos generating two-body interaction are modeled by one plus two-body embedded Gaussian orthogonal ensemble of random matrices with spin degree of freedom [called EGOE(1+2)-s]. Numerical calculations are used to demonstrate that, as lambda , the strength of the interaction (measured in the units of the average spacing of the single-particle levels defining the mean-field), increases, generically there is Poisson to GOE transition in level fluctuations, Breit-Wigner to Gaussian transition in strength functions (also called local density of states) and also a duality region where information entropy will be the same in both the mean-field and interaction defined basis. Spin dependence of the transition points lambda_{c} , lambdaF, and lambdad , respectively, is described using the propagator for the spectral variances and the formula for the propagator is derived. We further establish that the duality region corresponds to a region of thermalization. For this purpose we compared the single-particle entropy defined by the occupancies of the single-particle orbitals with thermodynamic entropy and information entropy for various lambda values and they are very close to each other at lambda=lambdad.
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Transit navigation through Northern Sea Route from satellite data and CMIP5 simulations
NASA Astrophysics Data System (ADS)
Khon, Vyacheslav C.; Mokhov, Igor I.; Semenov, Vladimir A.
2017-02-01
Rapid Arctic sea ice decline over the last few decades opens new perspectives for Arctic marine navigation. Further warming in the Arctic will promote the Northern Sea Route (NSR) as an alternative to the conventional Suez or Panama Canal routes for intercontinental shipping. Here we use both satellite data and CMIP5 ensemble of climate models to estimate the NSR transit window allowing intercontinental navigation between Atlantic and Pacific regions. To this end, we introduce a novel approach to calculate start and end dates of the navigation season along the NSR. We show that modern climate models are able to reproduce the mean time of the NSR transit window and its trend over the last few decades. The selected models demonstrate that the rate of increase of the NSR navigation season will slow down over the next few decades with the RCP4.5 scenario. By the end of the 21st century ensemble-mean estimates show an increase of the NSR transit window by about 4 and 6.5 months according to RCP4.5 and 8.5, respectively. Estimated trends for the end date of the navigation season are found to be stronger compared to those for the start date.
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An ensemble method for extracting adverse drug events from social media.
Liu, Jing; Zhao, Songzheng; Zhang, Xiaodi
2016-06-01
Because adverse drug events (ADEs) are a serious health problem and a leading cause of death, it is of vital importance to identify them correctly and in a timely manner. With the development of Web 2.0, social media has become a large data source for information on ADEs. The objective of this study is to develop a relation extraction system that uses natural language processing techniques to effectively distinguish between ADEs and non-ADEs in informal text on social media. We develop a feature-based approach that utilizes various lexical, syntactic, and semantic features. Information-gain-based feature selection is performed to address high-dimensional features. Then, we evaluate the effectiveness of four well-known kernel-based approaches (i.e., subset tree kernel, tree kernel, shortest dependency path kernel, and all-paths graph kernel) and several ensembles that are generated by adopting different combination methods (i.e., majority voting, weighted averaging, and stacked generalization). All of the approaches are tested using three data sets: two health-related discussion forums and one general social networking site (i.e., Twitter). When investigating the contribution of each feature subset, the feature-based approach attains the best area under the receiver operating characteristics curve (AUC) values, which are 78.6%, 72.2%, and 79.2% on the three data sets. When individual methods are used, we attain the best AUC values of 82.1%, 73.2%, and 77.0% using the subset tree kernel, shortest dependency path kernel, and feature-based approach on the three data sets, respectively. When using classifier ensembles, we achieve the best AUC values of 84.5%, 77.3%, and 84.5% on the three data sets, outperforming the baselines. Our experimental results indicate that ADE extraction from social media can benefit from feature selection. With respect to the effectiveness of different feature subsets, lexical features and semantic features can enhance the ADE extraction capability. Kernel-based approaches, which can stay away from the feature sparsity issue, are qualified to address the ADE extraction problem. Combining different individual classifiers using suitable combination methods can further enhance the ADE extraction effectiveness. Copyright © 2016 Elsevier B.V. All rights reserved.
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Self-averaging and weak ergodicity breaking of diffusion in heterogeneous media
NASA Astrophysics Data System (ADS)
Russian, Anna; Dentz, Marco; Gouze, Philippe
2017-08-01
Diffusion in natural and engineered media is quantified in terms of stochastic models for the heterogeneity-induced fluctuations of particle motion. However, fundamental properties such as ergodicity and self-averaging and their dependence on the disorder distribution are often not known. Here, we investigate these questions for diffusion in quenched disordered media characterized by spatially varying retardation properties, which account for particle retention due to physical or chemical interactions with the medium. We link self-averaging and ergodicity to the disorder sampling efficiency Rn, which quantifies the number of disorder realizations a noise ensemble may sample in a single disorder realization. Diffusion for disorder scenarios characterized by a finite mean transition time is ergodic and self-averaging for any dimension. The strength of the sample to sample fluctuations decreases with increasing spatial dimension. For an infinite mean transition time, particle motion is weakly ergodicity breaking in any dimension because single particles cannot sample the heterogeneity spectrum in finite time. However, even though the noise ensemble is not representative of the single-particle time statistics, subdiffusive motion in q ≥2 dimensions is self-averaging, which means that the noise ensemble in a single realization samples a representative part of the heterogeneity spectrum.
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Ensemble Atmospheric Properties of Small Planets around M Dwarfs
NASA Astrophysics Data System (ADS)
Guo, Xueying; Ballard, Sarah; Dragomir, Diana
2018-01-01
With the growing number of planets discovered by the Kepler mission and ground-base surveys, people start to try to understand the atmospheric features of those uncovered new worlds. While it has been found that hot Jupiters exhibit diverse atmosphere composition with both clear and cloudy/hazy atmosphere possible, similar studies on ensembles of smaller planets (Earth analogs) have been held up due to the faintness of most of their host stars. In this work, a sample of 20 Earth analogs of similar periods around M dwarfs with existing Kepler transit information and Spitzer observations is composed, complemented with previously studies GJ1214b and GJ1132b, as well as the recently announced 7 small planets in the TRAPPIST-1 system. We evaluate their transit depths with uncertainties on the Spitzer 4.5 micron band using the “pixel-level decorrelation” method, and together with their well analyzed Kepler data and Hubble data, we put constraints on their atmosphere haze slopes and cloud levels. Aside from improving the understanding of ensemble properties of small planets, this study will also provide clues of potential targets for detailed atmospheric studies using the upcoming James Webb Telescope.
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NASA Astrophysics Data System (ADS)
Huang, Yong; Wang, Kehong; Zhou, Zhilan; Zhou, Xiaoxiao; Fang, Jimi
2017-03-01
The arc of gas metal arc welding (GMAW) contains abundant information about its stability and droplet transition, which can be effectively characterized by extracting the arc electrical signals. In this study, ensemble empirical mode decomposition (EEMD) was used to evaluate the stability of electrical current signals. The welding electrical signals were first decomposed by EEMD, and then transformed to a Hilbert-Huang spectrum and a marginal spectrum. The marginal spectrum is an approximate distribution of amplitude with frequency of signals, and can be described by a marginal index. Analysis of various welding process parameters showed that the marginal index of current signals increased when the welding process was more stable, and vice versa. Thus EEMD combined with the marginal index can effectively uncover the stability and droplet transition of GMAW.
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Fixed points, stable manifolds, weather regimes, and their predictability.
Deremble, Bruno; D'Andrea, Fabio; Ghil, Michael
2009-12-01
In a simple, one-layer atmospheric model, we study the links between low-frequency variability and the model's fixed points in phase space. The model dynamics is characterized by the coexistence of multiple "weather regimes." To investigate the transitions from one regime to another, we focus on the identification of stable manifolds associated with fixed points. We show that these manifolds act as separatrices between regimes. We track each manifold by making use of two local predictability measures arising from the meteorological applications of nonlinear dynamics, namely, "bred vectors" and singular vectors. These results are then verified in the framework of ensemble forecasts issued from "clouds" (ensembles) of initial states. The divergence of the trajectories allows us to establish the connections between zones of low predictability, the geometry of the stable manifolds, and transitions between regimes.
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High-density amorphous ice: A path-integral simulation
NASA Astrophysics Data System (ADS)
Herrero, Carlos P.; Ramírez, Rafael
2012-09-01
Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Quantum nuclear motion is found to affect several observable properties of the amorphous solid. At low temperature (T = 50 K) the molar volume of HDA ice is found to increase by 6%, and the intramolecular O-H distance rises by 1.4% due to quantum motion. Peaks in the radial distribution function of HDA ice are broadened with respect to their classical expectancy. The bulk modulus, B, is found to rise linearly with the pressure, with a slope ∂B/∂P = 7.1. Our results are compared with those derived earlier from classical and path-integral simulations of HDA ice. We discuss similarities and discrepancies with those earlier simulations.
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Zhang, Jiayong; Zhang, Hongwu; Ye, Hongfei; Zheng, Yonggang
2016-09-07
A free-end adaptive nudged elastic band (FEA-NEB) method is presented for finding transition states on minimum energy paths, where the energy barrier is very narrow compared to the whole paths. The previously proposed free-end nudged elastic band method may suffer from convergence problems because of the kinks arising on the elastic band if the initial elastic band is far from the minimum energy path and weak springs are adopted. We analyze the origin of the formation of kinks and present an improved free-end algorithm to avoid the convergence problem. Moreover, by coupling the improved free-end algorithm and an adaptive strategy, we develop a FEA-NEB method to accurately locate the transition state with the elastic band cut off repeatedly and the density of images near the transition state increased. Several representative numerical examples, including the dislocation nucleation in a penta-twinned nanowire, the twin boundary migration under a shear stress, and the cross-slip of screw dislocation in face-centered cubic metals, are investigated by using the FEA-NEB method. Numerical results demonstrate both the stability and efficiency of the proposed method.
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NASA Astrophysics Data System (ADS)
Weber, Steven; Murch, K. W.; Chantasri, A.; Dressel, J.; Jordan, A. N.; Siddiqi, I.
2014-03-01
We use weak measurements to track individual quantum trajectories of a superconducting qubit embedded in a microwave cavity. Using a near-quantum-limited parametric amplifier, we selectively measure either the phase or amplitude of the cavity field, and thereby confine trajectories to either the equator or a meridian of the Bloch sphere. We analyze ensembles of trajectories to determine statistical properties such as the most likely path and most likely time connecting pre and post-selected quantum states. We compare our results with theoretical predictions derived from an action principle for continuous quantum measurement. Furthermore, by introducing a qubit drive, we investigate the interplay between unitary state evolution and non-unitary measurement dynamics. This work was supported by the IARPA CSQ program and the ONR.
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A New Look into the Effect of Large Drops on Radiative Transfer Process
NASA Technical Reports Server (NTRS)
Marshak, Alexander
2003-01-01
Recent studies indicate that a cloudy atmosphere absorbs more solar radiation than any current 1D or 3D radiation model can predict. The excess absorption is not large, perhaps 10-15 W/sq m or less, but any such systematic bias is of concern since radiative transfer models are assumed to be sufficiently accurate for remote sensing applications and climate modeling. The most natural explanation would be that models do not capture real 3D cloud structure and, as a consequence, their photon path lengths are too short. However, extensive calculations, using increasingly realistic 3D cloud structures, failed to produce photon paths long enough to explain the excess absorption. Other possible explanations have also been unsuccessful so, at this point, conventional models seem to offer no solution to this puzzle. The weakest link in conventional models is the way a size distribution of cloud particles is mathematically handled. Basically, real particles are replaced with a single average particle. This "ensemble assumption" assumes that all particle sizes are well represented in any given elementary volume. But the concentration of larger particles can be so low that this assumption is significantly violated. We show how a different mathematical route, using the concept of a cumulative distribution, avoids the ensemble assumption. The cumulative distribution has jumps, or steps, corresponding to the rarer sizes. These jumps result in an additional term, a kind of Green's function, in the solution of the radiative transfer equation. Solving the cloud radiative transfer equation with the measured particle distributions, described in a cumulative rather than an ensemble fashion, may lead to increased cloud absorption of the magnitude observed.
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Entropy criteria applied to pattern selection in systems with free boundaries
NASA Astrophysics Data System (ADS)
Kirkaldy, J. S.
1985-10-01
The steady state differential or integral equations which describe patterned dissipative structures, typically to be identified with first order phase transformation morphologies like isothermal pearlites, are invariably degenerate in one or more order parameters (the lamellar spacing in the pearlite case). It is often observed that a different pattern is attained at the steady state for each initial condition (the hysteresis or metastable case). Alternatively, boundary perturbations and internal fluctuations during transition up to, or at the steady state, destroy the path coherence. In this case a statistical ensemble of imperfect patterns often emerges which represents a fluctuating but recognizably patterned and unique average steady state. It is cases like cellular, lamellar pearlite, involving an assembly of individual cell patterns which are regularly perturbed by local fluctuation and growth processes, which concern us here. Such weakly fluctuating nonlinear steady state ensembles can be arranged in a thought experiment so as to evolve as subsystems linking two very large mass-energy reservoirs in isolation. Operating on this discontinuous thermodynamic ideal, Onsager’s principle of maximum path probability for isolated systems, which we interpret as a minimal time correlation function connecting subsystem and baths, identifies the stable steady state at a parametric minimum or maximum (or both) in the dissipation rate. This nonlinear principle is independent of the Principle of Minimum Dissipation which is applicable in the linear regime of irreversible thermodynamics. The statistical argument is equivalent to the weak requirement that the isolated system entropy as a function of time be differentiable to the second order despite the macroscopic pattern fluctuations which occur in the subsystem. This differentiability condition is taken for granted in classical stability theory based on the 2nd Law. The optimal principle as applied to isothermal and forced velocity pearlites (in this case maximal) possesses a Le Chatelier (perturbation) Principle which can be formulated exactly via Langer’s conjecture that “each lamella must grow in a direction which is perpendicular to the solidification front”. This is the first example of such an equivalence to be experimentally and theoretically recognized in nonlinear irreversible thermodynamics. A further application to binary solidification cells is reviewed. In this case the optimum in the dissipation is a minimum and the closure between theory and experiment is excellent. Other applications in thermal-hydraulics, biology, and solid state physics are briefy described.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wiebe, David J.
A transition duct system (10) for delivering hot-temperature gases from a plurality of combustors in a combustion turbine engine is provided. The system includes an exit piece (16) for each combustor. The exit piece may include a straight path segment (26) for receiving a gas flow from a respective combustor. A straight ceramic liner (40) may be inwardly disposed onto a metal outer shell (38) along the straight path segment of the exit piece. Structural arrangements are provided to securely attach the ceramic liner in the presence of substantial flow path pressurization. Cost-effective serviceability of the transition duct systems ismore » realizable since the liner can be readily removed and replaced as needed.« less
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Circuity analyses of HSR network and high-speed train paths in China
Zhao, Shuo; Huang, Jie; Shan, Xinghua
2017-01-01
Circuity, defined as the ratio of the shortest network distance to the Euclidean distance between one origin–destination (O-D) pair, can be adopted as a helpful evaluation method of indirect degrees of train paths. In this paper, the maximum circuity of the paths of operated trains is set to be the threshold value of the circuity of high-speed train paths. For the shortest paths of any node pairs, if their circuity is not higher than the threshold value, the paths can be regarded as the reasonable paths. With the consideration of a certain relative or absolute error, we cluster the reasonable paths on the basis of their inclusion relationship and the center path of each class represents a passenger transit corridor. We take the high-speed rail (HSR) network in China at the end of 2014 as an example, and obtain 51 passenger transit corridors, which are alternative sets of train paths. Furthermore, we analyze the circuity distribution of paths of all node pairs in the network. We find that the high circuity of train paths can be decreased with the construction of a high-speed railway line, which indicates that the structure of the HSR network in China tends to be more complete and the HSR network can make the Chinese railway network more efficient. PMID:28945757
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NASA Astrophysics Data System (ADS)
Pribram-Jones, Aurora
Warm dense matter (WDM) is a high energy phase between solids and plasmas, with characteristics of both. It is present in the centers of giant planets, within the earth's core, and on the path to ignition of inertial confinement fusion. The high temperatures and pressures of warm dense matter lead to complications in its simulation, as both classical and quantum effects must be included. One of the most successful simulation methods is density functional theory-molecular dynamics (DFT-MD). Despite great success in a diverse array of applications, DFT-MD remains computationally expensive and it neglects the explicit temperature dependence of electron-electron interactions known to exist within exact DFT. Finite-temperature density functional theory (FT DFT) is an extension of the wildly successful ground-state DFT formalism via thermal ensembles, broadening its quantum mechanical treatment of electrons to include systems at non-zero temperatures. Exact mathematical conditions have been used to predict the behavior of approximations in limiting conditions and to connect FT DFT to the ground-state theory. An introduction to FT DFT is given within the context of ensemble DFT and the larger field of DFT is discussed for context. Ensemble DFT is used to describe ensembles of ground-state and excited systems. Exact conditions in ensemble DFT and the performance of approximations depend on ensemble weights. Using an inversion method, exact Kohn-Sham ensemble potentials are found and compared to approximations. The symmetry eigenstate Hartree-exchange approximation is in good agreement with exact calculations because of its inclusion of an ensemble derivative discontinuity. Since ensemble weights in FT DFT are temperature-dependent Fermi weights, this insight may help develop approximations well-suited to both ground-state and FT DFT. A novel, highly efficient approach to free energy calculations, finite-temperature potential functional theory, is derived, which has the potential to transform the simulation of warm dense matter. As a semiclassical method, it connects the normally disparate regimes of cold condensed matter physics and hot plasma physics. This orbital-free approach captures the smooth classical density envelope and quantum density oscillations that are both crucial to accurate modeling of materials where temperature and pressure effects are influential.
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Ensemble Bayesian forecasting system Part I: Theory and algorithms
NASA Astrophysics Data System (ADS)
Herr, Henry D.; Krzysztofowicz, Roman
2015-05-01
The ensemble Bayesian forecasting system (EBFS), whose theory was published in 2001, is developed for the purpose of quantifying the total uncertainty about a discrete-time, continuous-state, non-stationary stochastic process such as a time series of stages, discharges, or volumes at a river gauge. The EBFS is built of three components: an input ensemble forecaster (IEF), which simulates the uncertainty associated with random inputs; a deterministic hydrologic model (of any complexity), which simulates physical processes within a river basin; and a hydrologic uncertainty processor (HUP), which simulates the hydrologic uncertainty (an aggregate of all uncertainties except input). It works as a Monte Carlo simulator: an ensemble of time series of inputs (e.g., precipitation amounts) generated by the IEF is transformed deterministically through a hydrologic model into an ensemble of time series of outputs, which is next transformed stochastically by the HUP into an ensemble of time series of predictands (e.g., river stages). Previous research indicated that in order to attain an acceptable sampling error, the ensemble size must be on the order of hundreds (for probabilistic river stage forecasts and probabilistic flood forecasts) or even thousands (for probabilistic stage transition forecasts). The computing time needed to run the hydrologic model this many times renders the straightforward simulations operationally infeasible. This motivates the development of the ensemble Bayesian forecasting system with randomization (EBFSR), which takes full advantage of the analytic meta-Gaussian HUP and generates multiple ensemble members after each run of the hydrologic model; this auxiliary randomization reduces the required size of the meteorological input ensemble and makes it operationally feasible to generate a Bayesian ensemble forecast of large size. Such a forecast quantifies the total uncertainty, is well calibrated against the prior (climatic) distribution of predictand, possesses a Bayesian coherence property, constitutes a random sample of the predictand, and has an acceptable sampling error-which makes it suitable for rational decision making under uncertainty.
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Giuliani, Alessandro; Tomita, Masaru
2010-01-01
Cell fate decision remarkably generates specific cell differentiation path among the multiple possibilities that can arise through the complex interplay of high-dimensional genome activities. The coordinated action of thousands of genes to switch cell fate decision has indicated the existence of stable attractors guiding the process. However, origins of the intracellular mechanisms that create “cellular attractor” still remain unknown. Here, we examined the collective behavior of genome-wide expressions for neutrophil differentiation through two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA). To overcome the difficulties of dealing with single gene expression noises, we grouped genes into ensembles and analyzed their expression dynamics in correlation space defined by Pearson correlation and mutual information. The standard deviation of correlation distributions of gene ensembles reduces when the ensemble size is increased following the inverse square root law, for both ensembles chosen randomly from whole genome and ranked according to expression variances across time. Choosing the ensemble size of 200 genes, we show the two probability distributions of correlations of randomly selected genes for atRA and DMSO responses overlapped after 48 hours, defining the neutrophil attractor. Next, tracking the ranked ensembles' trajectories, we noticed that only certain, not all, fall into the attractor in a fractal-like manner. The removal of these genome elements from the whole genomes, for both atRA and DMSO responses, destroys the attractor providing evidence for the existence of specific genome elements (named “genome vehicle”) responsible for the neutrophil attractor. Notably, within the genome vehicles, genes with low or moderate expression changes, which are often considered noisy and insignificant, are essential components for the creation of the neutrophil attractor. Further investigations along with our findings might provide a comprehensive mechanistic view of cell fate decision. PMID:20725638
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The forces on a single interacting Bose-Einstein condensate
NASA Astrophysics Data System (ADS)
Thu, Nguyen Van
2018-04-01
Using double parabola approximation for a single Bose-Einstein condensate confined between double slabs we proved that in grand canonical ensemble (GCE) the ground state with Robin boundary condition (BC) is favored, whereas in canonical ensemble (CE) our system undergoes from ground state with Robin BC to the one with Dirichlet BC in small-L region and vice versa for large-L region and phase transition in space of the ground state is the first order. The surface tension force and Casimir force are also considered in both CE and GCE in detail.
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Malolepsza, Edyta; Secor, Maxim; Keyes, Tom
2015-09-23
A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed for simulating first-order phase transitions. The properties of the isobaric gREM ensemble are discussed and a study is presented of the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. As a result, phase diagrams, critical parameters, and a law of corresponding states are obtained.
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Quantum chaos inside black holes
NASA Astrophysics Data System (ADS)
Addazi, Andrea
2017-06-01
We show how semiclassical black holes can be reinterpreted as an effective geometry, composed of a large ensemble of horizonless naked singularities (eventually smoothed at the Planck scale). We call these new items frizzy-balls, which can be rigorously defined by Euclidean path integral approach. This leads to interesting implications about information paradoxes. We demonstrate that infalling information will chaotically propagate inside this system before going to the full quantum gravity regime (Planck scale).
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Path statistics, memory, and coarse-graining of continuous-time random walks on networks
Kion-Crosby, Willow; Morozov, Alexandre V.
2015-01-01
Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states (for example, those employed in studies of molecular kinetics) or spatial disorder can give rise to memory and non-exponential distributions of waiting times and first-passage statistics. However, existing methods for analyzing CTRWs on complex energy landscapes do not address these effects. Here we use statistical mechanics of the nonequilibrium path ensemble to characterize first-passage CTRWs on networks with arbitrary connectivity, energy landscape, and waiting time distributions. Our approach can be applied to calculating higher moments (beyond the mean) of path length, time, and action, as well as statistics of any conservative or non-conservative force along a path. For homogeneous networks, we derive exact relations between length and time moments, quantifying the validity of approximating a continuous-time process with its discrete-time projection. For more general models, we obtain recursion relations, reminiscent of transfer matrix and exact enumeration techniques, to efficiently calculate path statistics numerically. We have implemented our algorithm in PathMAN (Path Matrix Algorithm for Networks), a Python script that users can apply to their model of choice. We demonstrate the algorithm on a few representative examples which underscore the importance of non-exponential distributions, memory, and coarse-graining in CTRWs. PMID:26646868
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Statistical mechanics of the vertex-cover problem
NASA Astrophysics Data System (ADS)
Hartmann, Alexander K.; Weigt, Martin
2003-10-01
We review recent progress in the study of the vertex-cover problem (VC). The VC belongs to the class of NP-complete graph theoretical problems, which plays a central role in theoretical computer science. On ensembles of random graphs, VC exhibits a coverable-uncoverable phase transition. Very close to this transition, depending on the solution algorithm, easy-hard transitions in the typical running time of the algorithms occur. We explain a statistical mechanics approach, which works by mapping the VC to a hard-core lattice gas, and then applying techniques such as the replica trick or the cavity approach. Using these methods, the phase diagram of the VC could be obtained exactly for connectivities c < e, where the VC is replica symmetric. Recently, this result could be confirmed using traditional mathematical techniques. For c > e, the solution of the VC exhibits full replica symmetry breaking. The statistical mechanics approach can also be used to study analytically the typical running time of simple complete and incomplete algorithms for the VC. Finally, we describe recent results for the VC when studied on other ensembles of finite- and infinite-dimensional graphs.
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Zhou, Yu; Pearson, John E; Auerbach, Anthony
2005-12-01
We derive the analytical form of a rate-equilibrium free-energy relationship (with slope Phi) for a bounded, linear chain of coupled reactions having arbitrary connecting rate constants. The results confirm previous simulation studies showing that Phi-values reflect the position of the perturbed reaction within the chain, with reactions occurring earlier in the sequence producing higher Phi-values than those occurring later in the sequence. The derivation includes an expression for the transmission coefficients of the overall reaction based on the rate constants of an arbitrary, discrete, finite Markov chain. The results indicate that experimental Phi-values can be used to calculate the relative heights of the energy barriers between intermediate states of the chain but provide no information about the energies of the wells along the reaction path. Application of the equations to the case of diliganded acetylcholine receptor channel gating suggests that the transition-state ensemble for this reaction is nearly flat. Although this mechanism accounts for many of the basic features of diliganded and unliganded acetylcholine receptor channel gating, the experimental rate-equilibrium free-energy relationships appear to be more linear than those predicted by the theory.
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Saleh, Noureldin; Ibrahim, Passainte; Saladino, Giorgio; Gervasio, Francesco Luigi; Clark, Timothy
2017-05-22
A generally applicable metadynamics scheme for predicting the free energy profile of ligand binding to G-protein-coupled receptors (GPCRs) is described. A common and effective collective variable (CV) has been defined using the ideally placed and highly conserved Trp6.48 as a reference point for ligand-GPCR distance measurement and the common orientation of GPCRs in the cell membrane. Using this single CV together with well-tempered multiple-walker metadynamics with a funnel-like boundary allows an efficient exploration of the entire ligand binding path from the extracellular medium to the orthosteric binding site, including vestibule and intermediate sites. The protocol can be used with X-ray structures or high-quality homology models (based on a high-quality template and after thorough refinement) for the receptor and is universally applicable to agonists, antagonists, and partial and reverse agonists. The root-mean-square error (RMSE) in predicted binding free energies for 12 diverse ligands in five receptors (a total of 23 data points) is surprisingly small (less than 1 kcal mol -1 ). The RMSEs for simulations that use receptor X-ray structures and homology models are very similar.
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ERIC Educational Resources Information Center
Furstenau, Sara
2005-01-01
In this contribution, the results of an empirical study on young immigrants' learning paths and school to job transition are presented. The study focused on the strategies of successful students from the Portuguese immigrant minority in Hamburg. One aim was to find out whether the young people could profit by their migration experiences and…
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Partial information, market efficiency, and anomalous continuous phase transition
NASA Astrophysics Data System (ADS)
Yang, Guang; Zheng, Wenzhi; Huang, Jiping
2014-04-01
It is a common belief in economics and social science that if there is more information available for agents to gather in a human system, the system can become more efficient. The belief can be easily understood according to the well-known efficient market hypothesis. In this work, we attempt to challenge this belief by investigating a complex adaptive system, which is modeled by a market-directed resource-allocation game with a directed random network. We conduct a series of controlled human experiments in the laboratory to show the reliability of the model design. As a result, we find that even under a small information concentration, the system can still almost reach the optimal (balanced) state. Furthermore, the ensemble average of the system’s fluctuation level goes through a continuous phase transition. This behavior means that in the second phase if too much information is shared among agents, the system’s stability will be harmed instead, which differs from the belief mentioned above. Also, at the transition point, the ensemble fluctuations of the fluctuation level remain at a low value. This phenomenon is in contrast to the textbook knowledge about continuous phase transitions in traditional physical systems, namely, fluctuations will rise abnormally around a transition point since the correlation length becomes infinite. Thus, this work is of potential value to a variety of fields, such as physics, economics, complexity science, and artificial intelligence.
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Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry.
Shi, Xuesong; Bonilla, Steve; Herschlag, Daniel; Harbury, Pehr
2015-01-01
The conformational ensemble of a macromolecule is the complete description of the macromolecule's solution structures and can reveal important aspects of macromolecular folding, recognition, and function. However, most experimental approaches determine an average or predominant structure, or follow transitions between states that each can only be described by an average structure. Ensembles have been extremely difficult to experimentally characterize. We present the unique advantages and capabilities of a new biophysical technique, X-ray scattering interferometry (XSI), for probing and quantifying structural ensembles. XSI measures the interference of scattered waves from two heavy metal probes attached site specifically to a macromolecule. A Fourier transform of the interference pattern gives the fractional abundance of different probe separations directly representing the multiple conformation states populated by the macromolecule. These probe-probe distance distributions can then be used to define the structural ensemble of the macromolecule. XSI provides accurate, calibrated distance in a model-independent fashion with angstrom scale sensitivity in distances. XSI data can be compared in a straightforward manner to atomic coordinates determined experimentally or predicted by molecular dynamics simulations. We describe the conceptual framework for XSI and provide a detailed protocol for carrying out an XSI experiment. © 2015 Elsevier Inc. All rights reserved.
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Ovchinnikov, Victor; Karplus, Martin
2014-01-01
A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes. PMID:24811667
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NASA Astrophysics Data System (ADS)
Ovchinnikov, Victor; Karplus, Martin
2014-05-01
A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15-20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.
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Microsecond protein dynamics observed at the single-molecule level
NASA Astrophysics Data System (ADS)
Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei
2015-07-01
How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape.
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Microsecond protein dynamics observed at the single-molecule level
Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei
2015-01-01
How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. PMID:26151767
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Quantum Synchronization of Two Ensembles of Atoms
NASA Astrophysics Data System (ADS)
Xu, Minghui; Tieri, David; Fine, Effie; Thompson, James; Holland, Murray
2014-05-01
We present a system that exhibits quantum synchronization as a modern analogue of the Huygens experiment which is implemented using state-of-the-art neutral atom lattice clocks of the highest precision. In particular, we study the correlated phase dynamics of two mesoscopic ensembles of atoms through their collective coupling to an optical cavity. We find a dynamical quantum phase transition induced by pump noise and cavity output-coupling. The spectral properties of the superradiant light emitted from the cavity show that at a critical pump rate the system undergoes a transition from the independent behavior of two disparate oscillators to the phase-locking that is the signature of quantum synchronization. Besides being of fundamental importance in nonequilibrium quantum many-body physics, this work could have broad implications for many practical applications of ultrastable lasers and precision measurements. This work was supported by the DARPA QuASAR program, the NSF, and NIST.
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Mesoscopic Fluctuations for the Thinned Circular Unitary Ensemble
NASA Astrophysics Data System (ADS)
Berggren, Tomas; Duits, Maurice
2017-09-01
In this paper we study the asymptotic behavior of mesoscopic fluctuations for the thinned Circular Unitary Ensemble. The effect of thinning is that the eigenvalues start to decorrelate. The decorrelation is stronger on the larger scales than on the smaller scales. We investigate this behavior by studying mesoscopic linear statistics. There are two regimes depending on the scale parameter and the thinning parameter. In one regime we obtain a CLT of a classical type and in the other regime we retrieve the CLT for CUE. The two regimes are separated by a critical line. On the critical line the limiting fluctuations are no longer Gaussian, but described by infinitely divisible laws. We argue that this transition phenomenon is universal by showing that the same transition and their laws appear for fluctuations of the thinned sine process in a growing box. The proofs are based on a Riemann-Hilbert problem for integrable operators.
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NASA Astrophysics Data System (ADS)
Naharudin, N.; Ahamad, M. S. S.; Sadullah, A. F. M.
2017-10-01
Every transit trip begins and ends with pedestrian travel. People need to walk to access the transit services. However, their choice to walk depends on many factors including the connectivity, level of comfort and safety. These factors can influence the pleasantness of riding the transit itself, especially during the first/last mile (FLM) journey. This had triggered few studies attempting to measure the pedestrian-friendliness a walking environment can offer. There were studies that implement the pedestrian experience on walking to assess the pedestrian-friendliness of a walking environment. There were also studies that use spatial analysis to measure it based on the path connectivity and accessibility to public facilities and amenities. Though both are good, but the perception-based studies and spatial analysis can be combined to derive more holistic results. This paper proposes a framework for selecting a pedestrian-friendly path for the FLM transit journey by using the two techniques (perception-based and spatial analysis). First, the degree of importance for the factors influencing a good walking environment will be aggregated by using Analytical Network Process (ANP) decision rules based on people's preferences on those factors. The weight will then be used as attributes in the GIS network analysis. Next, the network analysis will be performed to find a pedestrian-friendly walking route based on the priorities aggregated by ANP. It will choose routes passing through the preferred attributes accordingly. The final output is a map showing pedestrian-friendly walking path for the FLM transit journey.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wiebe, David J.
A transition duct system (10) for delivering hot-temperature gases from a plurality of combustors in a combustion turbine engine is provided. The system includes an exit piece (16) for each combustor. The exit piece may include a straight path segment (26) and an arcuate connecting segment (36). A respective straight metal liner (92) and an arcuate metal liner (94) may be each inwardly disposed onto a metal outer shell (38) along the straight path segment and the arcuate connecting segment (36) of the exit piece. Structural arrangements are provided to securely attach the respective liners in the presence of substantialmore » flow path pressurization. Cost-effective serviceability of the transition duct systems is realizable since the liners can be readily removed and replaced as needed.« less
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Kreck, Cara A; Mancera, Ricardo L
2014-02-20
Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.
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Stabilizing IkappaBalpha by "consensus" design.
Ferreiro, Diego U; Cervantes, Carla F; Truhlar, Stephanie M E; Cho, Samuel S; Wolynes, Peter G; Komives, Elizabeth A
2007-01-26
IkappaBalpha is the major regulator of transcription factor NF-kappaB function. The ankyrin repeat region of IkappaBalpha mediates specific interactions with NF-kappaB dimers, but ankyrin repeats 1, 5 and 6 display a highly dynamic character when not in complex with NF-kappaB. Using chemical denaturation, we show here that IkappaBalpha displays two folding transitions: a non-cooperative conversion under weak perturbation, and a major cooperative folding phase upon stronger insult. Taking advantage of a native Trp residue in ankyrin repeat (AR) 6 and engineered Trp residues in AR2, AR4 and AR5, we show that the cooperative transition involves AR2 and AR3, while the non-cooperative transition involves AR5 and AR6. The major structural transition can be affected by single amino acid substitutions converging to the "consensus" ankyrin repeat sequence, increasing the native state stability significantly. We further characterized the structural and dynamic properties of the native state ensemble of IkappaBalpha and the stabilized mutants by H/(2)H exchange mass spectrometry and NMR. The solution experiments were complemented with molecular dynamics simulations to elucidate the microscopic origins of the stabilizing effect of the consensus substitutions, which can be traced to the fast conformational dynamics of the folded ensemble.
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Kepler Mission: End-to-End System Demonstration
NASA Technical Reports Server (NTRS)
Borucki, William; Koch, D.; Dunham, E.; Jenkins, J.; Witteborn, F.; Updike, T.; DeVincenzi, Donald L. (Technical Monitor)
2000-01-01
A test facility has been constructed to demonstrate the capability of differential ensemble photometry to detect transits of Earth-size planets orbiting solar-like stars. The main objective is to determine the effects of various noise sources on the capability of a CCD photometer to maintain a system relative precision of 1 x $10^(-5)$ for mv = 12 stars in the presence of system-induced noise sources. The facility includes a simulated star field, fast optics to simulate the telescope, a thinned back-illuminated CCD similar to those to be used on the spacecraft and computers to perform the onboard control, data processing and extraction. The test structure is thermally and mechanically isolated so that each source of noise can be introduced in a controlled fashion and evaluated for its contribution to the total noise budget. The effects of pointing errors or a changing thermal environment are imposed by piezo-electric devices. Transits are injected by heating small wires crossing apertures in the star plate. Signals as small as those from terrestrial-size transits of solar-like stars are introduced to demonstrate that such planets can be detected under realistic noise conditions. Examples of imposing several noise sources and the resulting detectabilities are presented. These show that a differential ensemble photometric approach CCD photometer can readily detect signals associated with Earth-size transits.
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Perroud, Thomas D.; Bokoch, Michael P.; Zare, Richard N.
2005-01-01
We apply the photon counting histogram (PCH) model, a fluorescence technique with single-molecule sensitivity, to study pH-induced conformational changes of cytochrome c. PCH is able to distinguish different protein conformations based on the brightness of a fluorophore sensitive to its local environment. We label cytochrome c through its single free cysteine with tetramethylrhodamine-5-maleimide (TMR), a fluorophore with specific brightnesses that we associate with specific protein conformations. Ensemble measurements demonstrate two different fluorescence responses with increasing pH: (i) a decrease in fluorescence intensity caused by the alkaline transition of cytochrome c (pH 7.0–9.5), and (ii) an increase in intensity when the protein unfolds (pH 9.5–10.8). The magnitudes of these two responses depend strongly on the molar ratio of TMR used to label cytochrome c. Using PCH we determine that this effect arises from the proportion of a nonfunctional conformation in the sample, which can be differentiated from the functional conformation. We further determine the causes of each ensemble fluorescence response: (i) during the alkaline transition, the fluorophore enters a dark state and discrete conformations are observed, and (ii) as cytochrome c unfolds, the fluorophore incrementally brightens, but discrete conformations are no longer resolved. Moreover, we also show that functional TMR-cytochrome c undergoes a response of identical magnitude regardless of the proportion of nonfunctional protein in the sample. As expected for a technique with single-molecule sensitivity, we demonstrate that PCH can directly observe the most relevant conformation, unlike ensemble fluorometry. PMID:16314563
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NASA Astrophysics Data System (ADS)
Nymeyer, Hugh; Socci, Nicholas D.; Onuchic, José Nelson
2000-01-01
* Department of Physics, University of California at San Diego, La Jolla, CA 92093-0319; and § Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021 Edited by R. Stephen Berry, University of Chicago, Chicago, IL, and approved November 5, 1999 (received for review July 2, 1999) We present a method for determining structural properties of the ensemble of folding transition states from protein simulations. This method relies on thermodynamic quantities (free energies as a function of global reaction coordinates, such as the percentage of native contacts) and not on "kinetic" measurements (rates, transmission coefficients, complete trajectories); consequently, it requires fewer computational resources compared with otherapproaches, making it more suited to large and complex models. We explain the theoretical framework that underlies this method and use it to clarify the connection between the experimentally determined
value, a quantity determined by the ratio of rate and stability changes due to point mutations, and the average structure of the transition state ensemble. To determine the accuracy of this thermodynamic approach, we apply it to minimalist protein models and compare these results with the ones obtained by using the standard experimental procedure for determining values. We show that the accuracy of both methods depends sensitively on the amount of frustration. In particular, the results are similar when applied to models with minimal amounts of frustration, characteristic of rapid-folding, single-domain globular proteins. -
Program for narrow-band analysis of aircraft flyover noise using ensemble averaging techniques
NASA Technical Reports Server (NTRS)
Gridley, D.
1982-01-01
A package of computer programs was developed for analyzing acoustic data from an aircraft flyover. The package assumes the aircraft is flying at constant altitude and constant velocity in a fixed attitude over a linear array of ground microphones. Aircraft position is provided by radar and an option exists for including the effects of the aircraft's rigid-body attitude relative to the flight path. Time synchronization between radar and acoustic recording stations permits ensemble averaging techniques to be applied to the acoustic data thereby increasing the statistical accuracy of the acoustic results. Measured layered meteorological data obtained during the flyovers are used to compute propagation effects through the atmosphere. Final results are narrow-band spectra and directivities corrected for the flight environment to an equivalent static condition at a specified radius.
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NASA Astrophysics Data System (ADS)
Małolepsza, Edyta; Kim, Jaegil; Keyes, Tom
2015-05-01
Metastable β ice holds small guest molecules in stable gas hydrates, so its solid-liquid equilibrium is of interest. However, aqueous crystal-liquid transitions are very difficult to simulate. A new molecular dynamics algorithm generates trajectories in a generalized N P T ensemble and equilibrates states of coexisting phases with a selectable enthalpy. With replicas spanning the range between β ice and liquid water, we find the statistical temperature from the enthalpy histograms and characterize the transition by the entropy, introducing a general computational procedure for first-order transitions.
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Malolepsza, Edyta; Kim, Jaegil; Keyes, Tom
2015-04-28
Metastable β ice holds small guest molecules in stable gas hydrates, so its solid/liquid equilibrium is of interest. However, aqueous crystal/liquid transitions are very difficult to simulate. A new MD algorithm generates trajectories in a generalized NPT ensemble and equilibrates states of coexisting phases with a selectable enthalpy. Furthermore, with replicas spanning the range between β ice and liquid water we find the statistical temperature from the enthalpy histograms and characterize the transition by the entropy, introducing a general computational procedure for first-order transitions.
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Squeezing via two-photon transitions
NASA Astrophysics Data System (ADS)
Savage, C. M.; Walls, D. F.
1986-05-01
The squeezing spectrum for a cavity field mode interacting with an ensemble of three-level 'Lambda-configuration' atoms by an effective two-photon transition is calculated. The advantage of the three-level Lambda system as a squeezing medium, that is, optical nonlinearity without atomic saturation, has recently been pointed out by Reid, Walls, and Dalton. Perfect squeezing is predicted at the turning points for dispersive optical bistability and good squeezing for a range of other cases. Three-level ladder atoms interacting by an effective two-photon transition are also shown to give perfect squeezing in the dispersive limit.
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An iterative ensemble quasi-linear data assimilation approach for integrated reservoir monitoring
NASA Astrophysics Data System (ADS)
Li, J. Y.; Kitanidis, P. K.
2013-12-01
Reservoir forecasting and management are increasingly relying on an integrated reservoir monitoring approach, which involves data assimilation to calibrate the complex process of multi-phase flow and transport in the porous medium. The numbers of unknowns and measurements arising in such joint inversion problems are usually very large. The ensemble Kalman filter and other ensemble-based techniques are popular because they circumvent the computational barriers of computing Jacobian matrices and covariance matrices explicitly and allow nonlinear error propagation. These algorithms are very useful but their performance is not well understood and it is not clear how many realizations are needed for satisfactory results. In this presentation we introduce an iterative ensemble quasi-linear data assimilation approach for integrated reservoir monitoring. It is intended for problems for which the posterior or conditional probability density function is not too different from a Gaussian, despite nonlinearity in the state transition and observation equations. The algorithm generates realizations that have the potential to adequately represent the conditional probability density function (pdf). Theoretical analysis sheds light on the conditions under which this algorithm should work well and explains why some applications require very few realizations while others require many. This algorithm is compared with the classical ensemble Kalman filter (Evensen, 2003) and with Gu and Oliver's (2007) iterative ensemble Kalman filter on a synthetic problem of monitoring a reservoir using wellbore pressure and flux data.
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Random matrix theory for transition strengths: Applications and open questions
NASA Astrophysics Data System (ADS)
Kota, V. K. B.
2017-12-01
Embedded random matrix ensembles are generic models for describing statistical properties of finite isolated interacting quantum many-particle systems. A finite quantum system, induced by a transition operator, makes transitions from its states to the states of the same system or to those of another system. Examples are electromagnetic transitions (then the initial and final systems are same), nuclear beta and double beta decay (then the initial and final systems are different) and so on. Using embedded ensembles (EE), there are efforts to derive a good statistical theory for transition strengths. With m fermions (or bosons) in N mean-field single particle levels and interacting via two-body forces, we have with GOE embedding, the so called EGOE(1+2). Now, the transition strength density (transition strength multiplied by the density of states at the initial and final energies) is a convolution of the density generated by the mean-field one-body part with a bivariate spreading function due to the two-body interaction. Using the embedding U(N) algebra, it is established, for a variety of transition operators, that the spreading function, for sufficiently strong interactions, is close to a bivariate Gaussian. Also, as the interaction strength increases, the spreading function exhibits a transition from bivariate Breit-Wigner to bivariate Gaussian form. In appropriate limits, this EE theory reduces to the polynomial theory of Draayer, French and Wong on one hand and to the theory due to Flambaum and Izrailev for one-body transition operators on the other. Using spin-cutoff factors for projecting angular momentum, the theory is applied to nuclear matrix elements for neutrinoless double beta decay (NDBD). In this paper we will describe: (i) various developments in the EE theory for transition strengths; (ii) results for nuclear matrix elements for 130Te and 136Xe NDBD; (iii) important open questions in the current form of the EE theory.
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Quantum transitions through cosmological singularities
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bramberger, Sebastian F.; Lehners, Jean-Luc; Hertog, Thomas
2017-07-01
In a quantum theory of cosmology spacetime behaves classically only in limited patches of the configuration space on which the wave function of the universe is defined. Quantum transitions can connect classical evolution in different patches. Working in the saddle point approximation and in minisuperspace we compute quantum transitions connecting inflationary histories across a de Sitter like throat or a singularity. This supplies probabilities for how an inflating universe, when evolved backwards, transitions and branches into an ensemble of histories on the opposite side of a quantum bounce. Generalising our analysis to scalar potentials with negative regions we identify saddlemore » points describing a quantum transition between a classically contracting, crunching ekpyrotic phase and an inflationary universe.« less
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Quantum transitions through cosmological singularities
NASA Astrophysics Data System (ADS)
Bramberger, Sebastian F.; Hertog, Thomas; Lehners, Jean-Luc; Vreys, Yannick
2017-07-01
In a quantum theory of cosmology spacetime behaves classically only in limited patches of the configuration space on which the wave function of the universe is defined. Quantum transitions can connect classical evolution in different patches. Working in the saddle point approximation and in minisuperspace we compute quantum transitions connecting inflationary histories across a de Sitter like throat or a singularity. This supplies probabilities for how an inflating universe, when evolved backwards, transitions and branches into an ensemble of histories on the opposite side of a quantum bounce. Generalising our analysis to scalar potentials with negative regions we identify saddle points describing a quantum transition between a classically contracting, crunching ekpyrotic phase and an inflationary universe.
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Hong-Ou-Mandel Interference between Two Deterministic Collective Excitations in an Atomic Ensemble
NASA Astrophysics Data System (ADS)
Li, Jun; Zhou, Ming-Ti; Jing, Bo; Wang, Xu-Jie; Yang, Sheng-Jun; Jiang, Xiao; Mølmer, Klaus; Bao, Xiao-Hui; Pan, Jian-Wei
2016-10-01
We demonstrate deterministic generation of two distinct collective excitations in one atomic ensemble, and we realize the Hong-Ou-Mandel interference between them. Using Rydberg blockade we create single collective excitations in two different Zeeman levels, and we use stimulated Raman transitions to perform a beam-splitter operation between the excited atomic modes. By converting the atomic excitations into photons, the two-excitation interference is measured by photon coincidence detection with a visibility of 0.89(6). The Hong-Ou-Mandel interference witnesses an entangled NOON state of the collective atomic excitations, and we demonstrate its two times enhanced sensitivity to a magnetic field compared with a single excitation. Our work implements a minimal instance of boson sampling and paves the way for further multimode and multiexcitation studies with collective excitations of atomic ensembles.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.
2013-11-07
Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors inmore » equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.« less
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Coherent Rabi Dynamics of a Superradiant Spin Ensemble in a Microwave Cavity
NASA Astrophysics Data System (ADS)
Rose, B. C.; Tyryshkin, A. M.; Riemann, H.; Abrosimov, N. V.; Becker, P.; Pohl, H.-J.; Thewalt, M. L. W.; Itoh, K. M.; Lyon, S. A.
2017-07-01
We achieve the strong-coupling regime between an ensemble of phosphorus donor spins in a highly enriched 28Si crystal and a 3D dielectric resonator. Spins are polarized beyond Boltzmann equilibrium using spin-selective optical excitation of the no-phonon bound exciton transition resulting in N =3.6 ×1 013 unpaired spins in the ensemble. We observe a normal mode splitting of the spin-ensemble-cavity polariton resonances of 2 g √{N }=580 kHz (where each spin is coupled with strength g ) in a cavity with a quality factor of 75 000 (γ ≪κ ≈60 kHz , where γ and κ are the spin dephasing and cavity loss rates, respectively). The spin ensemble has a long dephasing time (T2*=9 μ s ) providing a wide window for viewing the dynamics of the coupled spin-ensemble-cavity system. The free-induction decay shows up to a dozen collapses and revivals revealing a coherent exchange of excitations between the superradiant state of the spin ensemble and the cavity at the rate g √{N }. The ensemble is found to evolve as a single large pseudospin according to the Tavis-Cummings model due to minimal inhomogeneous broadening and uniform spin-cavity coupling. We demonstrate independent control of the total spin and the initial Z projection of the psuedospin using optical excitation and microwave manipulation, respectively. We vary the microwave excitation power to rotate the pseudospin on the Bloch sphere and observe a long delay in the onset of the superradiant emission as the pseudospin approaches full inversion. This delay is accompanied by an abrupt π -phase shift in the peusdospin microwave emission. The scaling of this delay with the initial angle and the sudden phase shift are explained by the Tavis-Cummings model.
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Cendagorta, Joseph R; Bačić, Zlatko; Tuckerman, Mark E
2018-03-14
We introduce a scheme for approximating quantum time correlation functions numerically within the Feynman path integral formulation. Starting with the symmetrized version of the correlation function expressed as a discretized path integral, we introduce a change of integration variables often used in the derivation of trajectory-based semiclassical methods. In particular, we transform to sum and difference variables between forward and backward complex-time propagation paths. Once the transformation is performed, the potential energy is expanded in powers of the difference variables, which allows us to perform the integrals over these variables analytically. The manner in which this procedure is carried out results in an open-chain path integral (in the remaining sum variables) with a modified potential that is evaluated using imaginary-time path-integral sampling rather than requiring the generation of a large ensemble of trajectories. Consequently, any number of path integral sampling schemes can be employed to compute the remaining path integral, including Monte Carlo, path-integral molecular dynamics, or enhanced path-integral molecular dynamics. We believe that this approach constitutes a different perspective in semiclassical-type approximations to quantum time correlation functions. Importantly, we argue that our approximation can be systematically improved within a cumulant expansion formalism. We test this approximation on a set of one-dimensional problems that are commonly used to benchmark approximate quantum dynamical schemes. We show that the method is at least as accurate as the popular ring-polymer molecular dynamics technique and linearized semiclassical initial value representation for correlation functions of linear operators in most of these examples and improves the accuracy of correlation functions of nonlinear operators.
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NASA Astrophysics Data System (ADS)
Cendagorta, Joseph R.; Bačić, Zlatko; Tuckerman, Mark E.
2018-03-01
We introduce a scheme for approximating quantum time correlation functions numerically within the Feynman path integral formulation. Starting with the symmetrized version of the correlation function expressed as a discretized path integral, we introduce a change of integration variables often used in the derivation of trajectory-based semiclassical methods. In particular, we transform to sum and difference variables between forward and backward complex-time propagation paths. Once the transformation is performed, the potential energy is expanded in powers of the difference variables, which allows us to perform the integrals over these variables analytically. The manner in which this procedure is carried out results in an open-chain path integral (in the remaining sum variables) with a modified potential that is evaluated using imaginary-time path-integral sampling rather than requiring the generation of a large ensemble of trajectories. Consequently, any number of path integral sampling schemes can be employed to compute the remaining path integral, including Monte Carlo, path-integral molecular dynamics, or enhanced path-integral molecular dynamics. We believe that this approach constitutes a different perspective in semiclassical-type approximations to quantum time correlation functions. Importantly, we argue that our approximation can be systematically improved within a cumulant expansion formalism. We test this approximation on a set of one-dimensional problems that are commonly used to benchmark approximate quantum dynamical schemes. We show that the method is at least as accurate as the popular ring-polymer molecular dynamics technique and linearized semiclassical initial value representation for correlation functions of linear operators in most of these examples and improves the accuracy of correlation functions of nonlinear operators.
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Mixed-order phase transition in a minimal, diffusion-based spin model.
Fronczak, Agata; Fronczak, Piotr
2016-07-01
In this paper we exactly solve, within the grand canonical ensemble, a minimal spin model with the hybrid phase transition. We call the model diffusion based because its Hamiltonian can be recovered from a simple dynamic procedure, which can be seen as an equilibrium statistical mechanics representation of a biased random walk. We outline the derivation of the phase diagram of the model, in which the triple point has the hallmarks of the hybrid transition: discontinuity in the average magnetization and algebraically diverging susceptibilities. At this point, two second-order transition curves meet in equilibrium with the first-order curve, resulting in a prototypical mixed-order behavior.
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NASA Astrophysics Data System (ADS)
Li, Hui-Ling; Yang, Shu-Zheng; Zu, Xiao-Tao
2017-01-01
In the framework of holography, we survey the phase structure for a higher dimensional hairy black hole including the effects of the scalar field hair. It is worth emphasizing that, not only black hole entropy, but also entanglement entropy and two point correlation function exhibit the Van der Waals-like phase transition in a fixed scalar charge ensemble. Furthermore, by making use of numerical computation, we show that the Maxwell's equal area law is valid for the first order phase transition. In addition, we also discuss how the hair parameter affects the black hole's phase transition.
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Critical mingling and universal correlations in model binary active liquids
NASA Astrophysics Data System (ADS)
Bain, Nicolas; Bartolo, Denis
2017-06-01
Ensembles of driven or motile bodies moving along opposite directions are generically reported to self-organize into strongly anisotropic lanes. Here, building on a minimal model of self-propelled bodies targeting opposite directions, we first evidence a critical phase transition between a mingled state and a phase-separated lane state specific to active particles. We then demonstrate that the mingled state displays algebraic structural correlations also found in driven binary mixtures. Finally, constructing a hydrodynamic theory, we single out the physical mechanisms responsible for these universal long-range correlations typical of ensembles of oppositely moving bodies.
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Thermodynamic characterization of synchronization-optimized oscillator networks
NASA Astrophysics Data System (ADS)
Yanagita, Tatsuo; Ichinomiya, Takashi
2014-12-01
We consider a canonical ensemble of synchronization-optimized networks of identical oscillators under external noise. By performing a Markov chain Monte Carlo simulation using the Kirchhoff index, i.e., the sum of the inverse eigenvalues of the Laplacian matrix (as a graph Hamiltonian of the network), we construct more than 1 000 different synchronization-optimized networks. We then show that the transition from star to core-periphery structure depends on the connectivity of the network, and is characterized by the node degree variance of the synchronization-optimized ensemble. We find that thermodynamic properties such as heat capacity show anomalies for sparse networks.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Latypov, Ramil F.; Liu, Dingjiang; Jacob, Jaby
2010-01-12
Conformational properties of the folded and unfolded ensembles of human interleukin-1 receptor antagonist (IL-1ra) are strongly denaturant-dependent as evidenced by high-resolution two-dimensional nuclear magnetic resonance (NMR), limited proteolysis, and small-angle X-ray scattering (SAXS). The folded ensemble was characterized in detail in the presence of different urea concentrations by 1H-15N HSQC NMR. The {beta}-trefoil fold characteristic of native IL-1ra was preserved until the unfolding transition region beginning at 4 M urea. At the same time, a subset of native resonances disappeared gradually starting at low denaturant concentrations, indicating noncooperative changes in the folded state. Additional evidence of structural perturbations came frommore » the chemical shift analysis, nonuniform and bell-shaped peak intensity profiles, and limited proteolysis. In particular, the following nearby regions of the tertiary structure became progressively destabilized with increasing urea concentrations: the {beta}-hairpin interface of trefoils 1 and 2 and the H2a-H2 helical region. These regions underwent small-scale perturbations within the native baseline region in the absence of populated molten globule-like states. Similar regions were affected by elevated temperatures known to induce irreversible aggregation of IL-1ra. Further evidence of structural transitions invoking near-native conformations came from an optical spectroscopy analysis of its single-tryptophan variant W17A. The increase in the radius of gyration was associated with a single equilibrium unfolding transition in the case of two different denaturants, urea and guanidine hydrochloride (GuHCl). However, the compactness of urea- and GuHCl-unfolded molecules was comparable only at high denaturant concentrations and deviated under less denaturing conditions. Our results identified the role of conformational flexibility in IL-1ra aggregation and shed light on the nature of structural transitions within the folded ensembles of other {beta}-trefoil proteins, such as IL-1{beta} and hFGF-1.« less
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Data assimilation in the low noise regime
NASA Astrophysics Data System (ADS)
Weare, J.; Vanden-Eijnden, E.
2012-12-01
On-line data assimilation techniques such as ensemble Kalman filters and particle filters tend to lose accuracy dramatically when presented with an unlikely observation. Such observation may be caused by an unusually large measurement error or reflect a rare fluctuation in the dynamics of the system. Over a long enough span of time it becomes likely that one or several of these events will occur. In some cases they are signatures of the most interesting features of the underlying system and their prediction becomes the primary focus of the data assimilation procedure. The Kuroshio or Black Current that runs along the eastern coast of Japan is an example of just such a system. It undergoes infrequent but dramatic changes of state between a small meander during which the current remains close to the coast of Japan, and a large meander during which the current bulges away from the coast. Because of the important role that the Kuroshio plays in distributing heat and salinity in the surrounding region, prediction of these transitions is of acute interest. { Here we focus on a regime in which both the stochastic forcing on the system and the observational noise are small. In this setting large deviation theory can be used to understand why standard filtering methods fail and guide the design of the more effective data assimilation techniques. Motivated by our large deviations analysis we propose several data assimilation strategies capable of efficiently handling rare events such as the transitions of the Kuroshio. These techniques are tested on a model of the Kuroshio and shown to perform much better than standard filtering methods.Here the sequence of observations (circles) are taken directly from one of our Kuroshio model's transition events from the small meander to the large meander. We tested two new algorithms (Algorithms 3 and 4 in the legend) motivated by our large deviations analysis as well as a standard particle filter and an ensemble Kalman filter. The parameters of each algorithm are chosen so that their costs are comparable. The particle filter and an ensemble Kalman filter fail to accurately track the transition. Algorithms 3 and 4 maintain accuracy (and smaller scale resolution) throughout the transition.
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NASA Astrophysics Data System (ADS)
Yuvchenko, S. A.; Ushakova, E. V.; Pavlova, M. V.; Alonova, M. V.; Zimnyakov, D. A.
2018-04-01
We consider the practical realization of a new optical probe method of the random media which is defined as the reference-free path length interferometry with the intensity moments analysis. A peculiarity in the statistics of the spectrally selected fluorescence radiation in laser-pumped dye-doped random medium is discussed. Previously established correlations between the second- and the third-order moments of the intensity fluctuations in the random interference patterns, the coherence function of the probe radiation, and the path difference probability density for the interfering partial waves in the medium are confirmed. The correlations were verified using the statistical analysis of the spectrally selected fluorescence radiation emitted by a laser-pumped dye-doped random medium. Water solution of Rhodamine 6G was applied as the doping fluorescent agent for the ensembles of the densely packed silica grains, which were pumped by the 532 nm radiation of a solid state laser. The spectrum of the mean path length for a random medium was reconstructed.
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Sign phase transition in the problem of interfering directed paths
NASA Astrophysics Data System (ADS)
Baldwin, C. L.; Laumann, C. R.; Spivak, B.
2018-01-01
We investigate the statistical properties of interfering directed paths in disordered media. At long distance, the average sign of the sum over paths may tend to zero (sign disordered) or remain finite (sign ordered) depending on dimensionality and the concentration of negative scattering sites x . We show that in two dimensions the sign-ordered phase is unstable even for arbitrarily small x by identifying rare destabilizing events. In three dimensions, we present strong evidence that there is a sign phase transition at a finite xc>0 . These results have consequences for several different physical systems. In two-dimensional insulators at low temperature, the variable-range-hopping magnetoresistance is always negative, while in three dimensions, it changes sign at the point of the sign phase transition. We also show that in the sign-disordered regime a small magnetic field may enhance superconductivity in a random system of D -wave superconducting grains embedded in a metallic matrix. Finally, the existence of the sign phase transition in three dimensions implies new features in the spin-glass phase diagram at high temperature.
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Beckstein, Oliver; Denning, Elizabeth J.; Perilla, Juan R.; Woolf, Thomas B.
2009-01-01
Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free energy calculations and our new dynamic importance sampling (DIMS) molecular dynamics (MD) method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular four ionic bonds are identified that open in a sequential, zipper-like fashion and thus dominate the free energy landscape of the transition. Transitions between the closed and open conformations only have to overcome moderate free energy barriers. Unexpectedly, the closed and open state encompass broad free energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental FRET measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS-MD computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK. PMID:19751742
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Water dynamics in large and small reverse micelles: From two ensembles to collective behavior
Moilanen, David E.; Fenn, Emily E.; Wong, Daryl; Fayer, Michael D.
2009-01-01
The dynamics of water in Aerosol-OT reverse micelles are investigated with ultrafast infrared spectroscopy of the hydroxyl stretch. In large reverse micelles, the dynamics of water are separable into two ensembles: slow interfacial water and bulklike core water. As the reverse micelle size decreases, the slowing effect of the interface and the collective nature of water reorientation begin to slow the dynamics of the core water molecules. In the smallest reverse micelles, these effects dominate and all water molecules have the same long time reorientational dynamics. To understand and characterize the transition in the water dynamics from two ensembles to collective reorientation, polarization and frequency selective infrared pump-probe experiments are conducted on the complete range of reverse micelle sizes from a diameter of 1.6–20 nm. The crossover between two ensemble and collective reorientation occurs near a reverse micelle diameter of 4 nm. Below this size, the small number of confined water molecules and structural changes in the reverse micelle interface leads to homogeneous long time reorientation. PMID:19586114
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Xie, Zheng; Srividya, Narayanan; Sosnick, Tobin R.; Pan, Tao; Scherer, Norbert F.
2004-01-01
The equilibrium folding of the catalytic domain of Bacillus subtilis RNase P RNA is investigated by single-molecule fluorescence resonance energy transfer (FRET). Previous ensemble studies of this 255-nucleotide ribozyme described the equilibrium folding with two transitions, U-to-Ieq-to-N, and focused on the Ieq-to-N transition. The present study focuses on the U-to-Ieq transition. Comparative ensemble measurements of the ribozyme construct labeled with fluorescein at the 5′ end and Cy3 at the 3′ end show that modifications required for labeling do not interfere with folding and help to define the Mg2+ concentration range for the U-to-Ieq transition. Histogram analysis of the Mg2+-dependent single-molecule FRET efficiency reveals two previously undetermined folding intermediates. The single-molecule FRET trajectories exhibit non-two-state and nonergodic behaviors at intermediate Mg2+ concentrations on the time scale of seconds. The trajectories at intermediate Mg2+ concentrations are classified into five classes based on three FRET levels and their dynamics of interconversion within the measured time range. This heterogeneity, together with the observation of “nonsudden jump” FRET transitions, indicates that the early folding steps of this ribozyme involve a series of intermediates with different degrees of kinetic isolation and that folding occurs under kinetic control and involves many “local” conformational switches. A free energy contour is constructed to illustrate the complex folding surface. PMID:14704266
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On Certain Wronskians of Multiple Orthogonal Polynomials
NASA Astrophysics Data System (ADS)
Zhang, Lun; Filipuk, Galina
2014-11-01
We consider determinants of Wronskian type whose entries are multiple orthogonal polynomials associated with a path connecting two multi-indices. By assuming that the weight functions form an algebraic Chebyshev (AT) system, we show that the polynomials represented by the Wronskians keep a constant sign in some cases, while in some other cases oscillatory behavior appears, which generalizes classical results for orthogonal polynomials due to Karlin and Szegő. There are two applications of our results. The first application arises from the observation that the m-th moment of the average characteristic polynomials for multiple orthogonal polynomial ensembles can be expressed as a Wronskian of the type II multiple orthogonal polynomials. Hence, it is straightforward to obtain the distinct behavior of the moments for odd and even m in a special multiple orthogonal ensemble - the AT ensemble. As the second application, we derive some Turán type inequalities for m! ultiple Hermite and multiple Laguerre polynomials (of two kinds). Finally, we study numerically the geometric configuration of zeros for the Wronskians of these multiple orthogonal polynomials. We observe that the zeros have regular configurations in the complex plane, which might be of independent interest.
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How Accurate Are Transition States from Simulations of Enzymatic Reactions?
2015-01-01
The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics. PMID:24860275
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National Centers for Environmental Prediction
Statistics Observational Data Processing Data Assimilation Monsoon Desk Model Transition Seminars Seminar (CFS) HURRICANE WEATHER RESEARCH and FORECASTING (HWRF) GLOBAL ENSEMBLE FORECAST SYSTEM (GEFS) NATIONAL Climate Prediction (NCWCP) 5830 University Research Court College Park, MD 20740 Page Author: EMC
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Hippocampal Sharp Wave Bursts Coincide with Neocortical "Up-State" Transitions
ERIC Educational Resources Information Center
Battaglia, Francesco P.; Sutherland, Gary R.; McNaughton, Bruce L.
2004-01-01
The sleeping neocortex shows nested oscillatory activity in different frequency ranges, characterized by fluctuations between "up-states" and "down-states." High-density neuronal ensemble recordings in rats now reveal the interaction between synchronized activity in the hippocampus and neocortex: Electroencephalographic sharp…
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Hefron, Ryan; Borghetti, Brett; Schubert Kabban, Christine; Christensen, James; Estepp, Justin
2018-04-26
Applying deep learning methods to electroencephalograph (EEG) data for cognitive state assessment has yielded improvements over previous modeling methods. However, research focused on cross-participant cognitive workload modeling using these techniques is underrepresented. We study the problem of cross-participant state estimation in a non-stimulus-locked task environment, where a trained model is used to make workload estimates on a new participant who is not represented in the training set. Using experimental data from the Multi-Attribute Task Battery (MATB) environment, a variety of deep neural network models are evaluated in the trade-space of computational efficiency, model accuracy, variance and temporal specificity yielding three important contributions: (1) The performance of ensembles of individually-trained models is statistically indistinguishable from group-trained methods at most sequence lengths. These ensembles can be trained for a fraction of the computational cost compared to group-trained methods and enable simpler model updates. (2) While increasing temporal sequence length improves mean accuracy, it is not sufficient to overcome distributional dissimilarities between individuals’ EEG data, as it results in statistically significant increases in cross-participant variance. (3) Compared to all other networks evaluated, a novel convolutional-recurrent model using multi-path subnetworks and bi-directional, residual recurrent layers resulted in statistically significant increases in predictive accuracy and decreases in cross-participant variance.
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Hefron, Ryan; Borghetti, Brett; Schubert Kabban, Christine; Christensen, James; Estepp, Justin
2018-01-01
Applying deep learning methods to electroencephalograph (EEG) data for cognitive state assessment has yielded improvements over previous modeling methods. However, research focused on cross-participant cognitive workload modeling using these techniques is underrepresented. We study the problem of cross-participant state estimation in a non-stimulus-locked task environment, where a trained model is used to make workload estimates on a new participant who is not represented in the training set. Using experimental data from the Multi-Attribute Task Battery (MATB) environment, a variety of deep neural network models are evaluated in the trade-space of computational efficiency, model accuracy, variance and temporal specificity yielding three important contributions: (1) The performance of ensembles of individually-trained models is statistically indistinguishable from group-trained methods at most sequence lengths. These ensembles can be trained for a fraction of the computational cost compared to group-trained methods and enable simpler model updates. (2) While increasing temporal sequence length improves mean accuracy, it is not sufficient to overcome distributional dissimilarities between individuals’ EEG data, as it results in statistically significant increases in cross-participant variance. (3) Compared to all other networks evaluated, a novel convolutional-recurrent model using multi-path subnetworks and bi-directional, residual recurrent layers resulted in statistically significant increases in predictive accuracy and decreases in cross-participant variance. PMID:29701668
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NASA Technical Reports Server (NTRS)
Hizanidis, Kyriakos; Vlahos, L.; Polymilis, C.
1989-01-01
The relativistic motion of an ensemble of electrons in an intense monochromatic electromagnetic wave propagating obliquely in a uniform external magnetic field is studied. The problem is formulated from the viewpoint of Hamiltonian theory and the Fokker-Planck-Kolmogorov approach analyzed by Hizanidis (1989), leading to a one-dimensional diffusive acceleration along paths of constant zeroth-order generalized Hamiltonian. For values of the wave amplitude and the propagating angle inside the analytically predicted stochastic region, the numerical results suggest that the diffusion probes proceeds in stages. In the first stage, the electrons are accelerated to relatively high energies by sampling the first few overlapping resonances one by one. During that stage, the ensemble-average square deviation of the variable involved scales quadratically with time. During the second stage, they scale linearly with time. For much longer times, deviation from linear scaling slowly sets in.
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Quantum storage of orbital angular momentum entanglement in an atomic ensemble.
Ding, Dong-Sheng; Zhang, Wei; Zhou, Zhi-Yuan; Shi, Shuai; Xiang, Guo-Yong; Wang, Xi-Shi; Jiang, Yun-Kun; Shi, Bao-Sen; Guo, Guang-Can
2015-02-06
Constructing a quantum memory for a photonic entanglement is vital for realizing quantum communication and network. Because of the inherent infinite dimension of orbital angular momentum (OAM), the photon's OAM has the potential for encoding a photon in a high-dimensional space, enabling the realization of high channel capacity communication. Photons entangled in orthogonal polarizations or optical paths had been stored in a different system, but there have been no reports on the storage of a photon pair entangled in OAM space. Here, we report the first experimental realization of storing an entangled OAM state through the Raman protocol in a cold atomic ensemble. We reconstruct the density matrix of an OAM entangled state with a fidelity of 90.3%±0.8% and obtain the Clauser-Horne-Shimony-Holt inequality parameter S of 2.41±0.06 after a programed storage time. All results clearly show the preservation of entanglement during the storage.
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Asymptotic Linear Spectral Statistics for Spiked Hermitian Random Matrices
NASA Astrophysics Data System (ADS)
Passemier, Damien; McKay, Matthew R.; Chen, Yang
2015-07-01
Using the Coulomb Fluid method, this paper derives central limit theorems (CLTs) for linear spectral statistics of three "spiked" Hermitian random matrix ensembles. These include Johnstone's spiked model (i.e., central Wishart with spiked correlation), non-central Wishart with rank-one non-centrality, and a related class of non-central matrices. For a generic linear statistic, we derive simple and explicit CLT expressions as the matrix dimensions grow large. For all three ensembles under consideration, we find that the primary effect of the spike is to introduce an correction term to the asymptotic mean of the linear spectral statistic, which we characterize with simple formulas. The utility of our proposed framework is demonstrated through application to three different linear statistics problems: the classical likelihood ratio test for a population covariance, the capacity analysis of multi-antenna wireless communication systems with a line-of-sight transmission path, and a classical multiple sample significance testing problem.
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Genuine non-self-averaging and ultraslow convergence in gelation.
Cho, Y S; Mazza, M G; Kahng, B; Nagler, J
2016-08-01
In irreversible aggregation processes droplets or polymers of microscopic size successively coalesce until a large cluster of macroscopic scale forms. This gelation transition is widely believed to be self-averaging, meaning that the order parameter (the relative size of the largest connected cluster) attains well-defined values upon ensemble averaging with no sample-to-sample fluctuations in the thermodynamic limit. Here, we report on anomalous gelation transition types. Depending on the growth rate of the largest clusters, the gelation transition can show very diverse patterns as a function of the control parameter, which includes multiple stochastic discontinuous transitions, genuine non-self-averaging and ultraslow convergence of the transition point. Our framework may be helpful in understanding and controlling gelation.
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Sensitivity to perturbations and quantum phase transitions.
Wisniacki, D A; Roncaglia, A J
2013-05-01
The local density of states or its Fourier transform, usually called fidelity amplitude, are important measures of quantum irreversibility due to imperfect evolution. In this Rapid Communication we study both quantities in a paradigmatic many body system, the Dicke Hamiltonian, where a single-mode bosonic field interacts with an ensemble of N two-level atoms. This model exhibits a quantum phase transition in the thermodynamic limit, while for finite instances the system undergoes a transition from quasi-integrability to quantum chaotic. We show that the width of the local density of states clearly points out the imprints of the transition from integrability to chaos but no trace remains of the quantum phase transition. The connection with the decay of the fidelity amplitude is also established.
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Role of Forcing Uncertainty and Background Model Error Characterization in Snow Data Assimilation
NASA Technical Reports Server (NTRS)
Kumar, Sujay V.; Dong, Jiarul; Peters-Lidard, Christa D.; Mocko, David; Gomez, Breogan
2017-01-01
Accurate specification of the model error covariances in data assimilation systems is a challenging issue. Ensemble land data assimilation methods rely on stochastic perturbations of input forcing and model prognostic fields for developing representations of input model error covariances. This article examines the limitations of using a single forcing dataset for specifying forcing uncertainty inputs for assimilating snow depth retrievals. Using an idealized data assimilation experiment, the article demonstrates that the use of hybrid forcing input strategies (either through the use of an ensemble of forcing products or through the added use of the forcing climatology) provide a better characterization of the background model error, which leads to improved data assimilation results, especially during the snow accumulation and melt-time periods. The use of hybrid forcing ensembles is then employed for assimilating snow depth retrievals from the AMSR2 (Advanced Microwave Scanning Radiometer 2) instrument over two domains in the continental USA with different snow evolution characteristics. Over a region near the Great Lakes, where the snow evolution tends to be ephemeral, the use of hybrid forcing ensembles provides significant improvements relative to the use of a single forcing dataset. Over the Colorado headwaters characterized by large snow accumulation, the impact of using the forcing ensemble is less prominent and is largely limited to the snow transition time periods. The results of the article demonstrate that improving the background model error through the use of a forcing ensemble enables the assimilation system to better incorporate the observational information.
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NASA Astrophysics Data System (ADS)
Bañados, Máximo; Düring, Gustavo; Faraggi, Alberto; Reyes, Ignacio A.
2017-08-01
We study the thermodynamic phase diagram of three-dimensional s l (N ;R ) higher spin black holes. By analyzing the semiclassical partition function we uncover a rich structure that includes Hawking-Page transitions to the AdS3 vacuum, first order phase transitions among black hole states, and a second order critical point. Our analysis is explicit for N =4 but we extrapolate some of our conclusions to arbitrary N . In particular, we argue that even N is stable in the ensemble under consideration but odd N is not.
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NASA Technical Reports Server (NTRS)
Thomas, Randy; Stueber, Thomas J.
2013-01-01
The System Identification (SysID) Rack is a real-time hardware-in-the-loop data acquisition (DAQ) and control instrument rack that was designed and built to support inlet testing in the NASA Glenn Research Center 10- by 10-Foot Supersonic Wind Tunnel. This instrument rack is used to support experiments on the Combined-Cycle Engine Large-Scale Inlet for Mode Transition Experiment (CCE? LIMX). The CCE?LIMX is a testbed for an integrated dual flow-path inlet configuration with the two flow paths in an over-and-under arrangement such that the high-speed flow path is located below the lowspeed flow path. The CCE?LIMX includes multiple actuators that are designed to redirect airflow from one flow path to the other; this action is referred to as "inlet mode transition." Multiple phases of experiments have been planned to support research that investigates inlet mode transition: inlet characterization (Phase-1) and system identification (Phase-2). The SysID Rack hardware design met the following requirements to support Phase-1 and Phase-2 experiments: safely and effectively move multiple actuators individually or synchronously; sample and save effector control and position sensor feedback signals; automate control of actuator positioning based on a mode transition schedule; sample and save pressure sensor signals; and perform DAQ and control processes operating at 2.5 KHz. This document describes the hardware components used to build the SysID Rack including their function, specifications, and system interface. Furthermore, provided in this document are a SysID Rack effectors signal list (signal flow); system identification experiment setup; illustrations indicating a typical SysID Rack experiment; and a SysID Rack performance overview for Phase-1 and Phase-2 experiments. The SysID Rack described in this document was a useful tool to meet the project objectives.
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Realization of a multipath ultrasonic gas flowmeter based on transit-time technique.
Chen, Qiang; Li, Weihua; Wu, Jiangtao
2014-01-01
A microcomputer-based ultrasonic gas flowmeter with transit-time method is presented. Modules of the flowmeter are designed systematically, including the acoustic path arrangement, ultrasound emission and reception module, transit-time measurement module, the software and so on. Four 200 kHz transducers forming two acoustic paths are used to send and receive ultrasound simultaneously. The synchronization of the transducers can eliminate the influence caused by the inherent switch time in simple chord flowmeter. The distribution of the acoustic paths on the mechanical apparatus follows the Tailored integration, which could reduce the inherent error by 2-3% compared with the Gaussian integration commonly used in the ultrasonic flowmeter now. This work also develops timing modules to determine the flight time of the acoustic signal. The timing mechanism is different from the traditional method. The timing circuit here adopts high capability chip TDC-GP2, with the typical resolution of 50 ps. The software of Labview is used to receive data from the circuit and calculate the gas flow value. Finally, the two paths flowmeter has been calibrated and validated on the test facilities for air flow in Shaanxi Institute of Measurement & Testing. Copyright © 2013 Elsevier B.V. All rights reserved.
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Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.
2015-01-01
The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815
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NASA Astrophysics Data System (ADS)
Peng, Yan; Wang, Bin; Liu, Yunqi
2018-03-01
We study the asymptotically flat quasi-local black hole/hairy black hole model with nonzero mass of the scalar field. We disclose effects of the scalar mass on transitions in a grand canonical ensemble with condensation behaviors of the parameter ψ 2, which is similar to approaches in holographic theories. We find that a more negative scalar mass makes the phase transition easier. We also obtain the analytical relation ψ 2∝ (Tc-T)^{1/2} around the critical phase transition points, implying a second order phase transition. Besides the parameter ψ 2, we show that metric solutions can be used to disclose properties of the transitions. In this work, we observe that phase transitions in a box are strikingly similar to holographic transitions in AdS gravity and the similarity provides insights into holographic theories.
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Shear-stress fluctuations and relaxation in polymer glasses
NASA Astrophysics Data System (ADS)
Kriuchevskyi, I.; Wittmer, J. P.; Meyer, H.; Benzerara, O.; Baschnagel, J.
2018-01-01
We investigate by means of molecular dynamics simulation a coarse-grained polymer glass model focusing on (quasistatic and dynamical) shear-stress fluctuations as a function of temperature T and sampling time Δ t . The linear response is characterized using (ensemble-averaged) expectation values of the contributions (time averaged for each shear plane) to the stress-fluctuation relation μsf for the shear modulus and the shear-stress relaxation modulus G (t ) . Using 100 independent configurations, we pay attention to the respective standard deviations. While the ensemble-averaged modulus μsf(T ) decreases continuously with increasing T for all Δ t sampled, its standard deviation δ μsf(T ) is nonmonotonic with a striking peak at the glass transition. The question of whether the shear modulus is continuous or has a jump singularity at the glass transition is thus ill posed. Confirming the effective time-translational invariance of our systems, the Δ t dependence of μsf and related quantities can be understood using a weighted integral over G (t ) .
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Evaluation of Rutter Sigma S6 Ice Navigation Radar on USCGC Healy during Arctic Shield 2014
2015-03-01
useful in making decisions about the pressure ridges ahead of time instead of making an immediate decision. Figure 33. CG radar display of... use the radar to help chart an efficient path through an ice field to reduce transit time and fuel expenses. This includes a clear picture of the ice...a ship would be able to use the radar to help chart an efficient path through an ice field to reduce transit time and fuel expenses. This includes
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Are atmospheric surface layer flows ergodic?
NASA Astrophysics Data System (ADS)
Higgins, Chad W.; Katul, Gabriel G.; Froidevaux, Martin; Simeonov, Valentin; Parlange, Marc B.
2013-06-01
The transposition of atmospheric turbulence statistics from the time domain, as conventionally sampled in field experiments, is explained by the so-called ergodic hypothesis. In micrometeorology, this hypothesis assumes that the time average of a measured flow variable represents an ensemble of independent realizations from similar meteorological states and boundary conditions. That is, the averaging duration must be sufficiently long to include a large number of independent realizations of the sampled flow variable so as to represent the ensemble. While the validity of the ergodic hypothesis for turbulence has been confirmed in laboratory experiments, and numerical simulations for idealized conditions, evidence for its validity in the atmospheric surface layer (ASL), especially for nonideal conditions, continues to defy experimental efforts. There is some urgency to make progress on this problem given the proliferation of tall tower scalar concentration networks aimed at constraining climate models yet are impacted by nonideal conditions at the land surface. Recent advancements in water vapor concentration lidar measurements that simultaneously sample spatial and temporal series in the ASL are used to investigate the validity of the ergodic hypothesis for the first time. It is shown that ergodicity is valid in a strict sense above uniform surfaces away from abrupt surface transitions. Surprisingly, ergodicity may be used to infer the ensemble concentration statistics of a composite grass-lake system using only water vapor concentration measurements collected above the sharp transition delineating the lake from the grass surface.
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Exploring first-order phase transitions with population annealing
NASA Astrophysics Data System (ADS)
Barash, Lev Yu.; Weigel, Martin; Shchur, Lev N.; Janke, Wolfhard
2017-03-01
Population annealing is a hybrid of sequential and Markov chain Monte Carlo methods geared towards the efficient parallel simulation of systems with complex free-energy landscapes. Systems with first-order phase transitions are among the problems in computational physics that are difficult to tackle with standard methods such as local-update simulations in the canonical ensemble, for example with the Metropolis algorithm. It is hence interesting to see whether such transitions can be more easily studied using population annealing. We report here our preliminary observations from population annealing runs for the two-dimensional Potts model with q > 4, where it undergoes a first-order transition.
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Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes
Schramm, Vern L.
2017-01-01
Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein’s dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states. PMID:21675920
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Optical Precursor with Four-Wave Mixing and Storage Based on a Cold-Atom Ensemble
NASA Astrophysics Data System (ADS)
Ding, Dong-Sheng; Jiang, Yun Kun; Zhang, Wei; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can
2015-03-01
We observed optical precursors in four-wave mixing based on a cold-atom gas. Optical precursors appear at the edges of pulses of the generated optical field, and propagate through the atomic medium without absorption. Theoretical analysis suggests that these precursors correspond to high-frequency components of the signal pulse, which means the atoms cannot respond quickly to rapid changes in the electromagnetic field. In contrast, the low-frequency signal components are absorbed by the atoms during transmission. We also showed experimentally that the backward precursor can be stored using a Raman transition of the atomic ensemble and retrieved later.
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Wetting transition on patterned surfaces: transition states and energy barriers.
Ren, Weiqing
2014-03-18
We study the wetting transition on microstructured hydrophobic surfaces. We use the string method [J. Chem. Phys. 2007, 126, 164103; J. Chem. Phys. 2013, 138, 134105] to accurately compute the transition states, the energy barriers, and the minimum energy paths for the wetting transition from the Cassie-Baxter state to the Wenzel state. Numerical results are obtained for the wetting of a hydrophobic surface textured with a square lattice of pillars. It is found that the wetting of the solid substrate occurs via infiltration of the liquid in a single groove, followed by lateral propagation of the liquid front. The propagation of the liquid front proceeds in a stepwise manner, and a zipping mechanism is observed during the infiltration of each layer. The minimum energy path for the wetting transition goes through a sequence of intermediate metastable states, whose wetted areas reflect the microstructure of the patterned surface. We also study the dependence of the energy barrier on the drop size and the gap between the pillars.
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Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
Juraszek, J.; Bolhuis, P. G.
2006-01-01
We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding. PMID:17035504
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Vassall, Kenrick A; Jenkins, Andrew D; Bamm, Vladimir V; Harauz, George
2015-05-22
The intrinsically disordered, 18.5-kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that is essential to proper myelin formation in the central nervous system. MBP acts in oligodendrocytes both to adjoin membrane leaflets to each other in forming myelin and as a hub in numerous protein-protein and protein-membrane interaction networks. Like many intrinsically disordered proteins (IDPs), MBP multifunctionality arises from its high conformational plasticity and its ability to undergo reversible disorder-to-order transitions. One such transition is the disorder-to-α-helical conformational change that is induced upon MBP-membrane binding. Here, we have investigated the disorder-to-α-helical transition of MBP-derived α-peptides and the full-length 18.5-kDa protein. This transition was induced through titration of the membrane-mimetic solvent trifluoroethanol into both protein and peptide solutions, and conformational change was monitored using circular dichroism spectroscopy, 1-anilinonaphthalene-8-sulfonic acid binding, tryptophan fluorescence quenching, and Förster (fluorescence) resonance energy transfer measurements. The data suggest that the disorder-to-α-helical transition of MBP follows a 3-state model: disordered↔intermediate↔α-helical, with each of the identified equilibrium states likely representing a conformational ensemble. The disordered state is characterized by slight compaction with little regular secondary structure, whereas the intermediate is also disordered but globally more compact. Surprisingly, the α-helical conformation is less compact than the intermediate. This study suggests that multifunctionality in MBP could arise from differences in the population of energetically distinct ensembles under different conditions and also provides an example of an IDP that undergoes cooperative global conformation change. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Near-optimal energy transitions for energy-state trajectories of hypersonic aircraft
NASA Technical Reports Server (NTRS)
Ardema, M. D.; Bowles, J. V.; Terjesen, E. J.; Whittaker, T.
1992-01-01
A problem of the instantaneous energy transition that occurs in energy-state approximation is considered. The transitions are modeled as a sequence of two load-factor bounded paths (either climb-dive or dive-climb). The boundary-layer equations associated with the energy-state dynamic model are analyzed to determine the precise location of the transition.
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Reliable Transition State Searches Integrated with the Growing String Method.
Zimmerman, Paul
2013-07-09
The growing string method (GSM) is highly useful for locating reaction paths connecting two molecular intermediates. GSM has often been used in a two-step procedure to locate exact transition states (TS), where GSM creates a quality initial structure for a local TS search. This procedure and others like it, however, do not always converge to the desired transition state because the local search is sensitive to the quality of the initial guess. This article describes an integrated technique for simultaneous reaction path and exact transition state search. This is achieved by implementing an eigenvector following optimization algorithm in internal coordinates with Hessian update techniques. After partial convergence of the string, an exact saddle point search begins under the constraint that the maximized eigenmode of the TS node Hessian has significant overlap with the string tangent near the TS. Subsequent optimization maintains connectivity of the string to the TS as well as locks in the TS direction, all but eliminating the possibility that the local search leads to the wrong TS. To verify the robustness of this approach, reaction paths and TSs are found for a benchmark set of more than 100 elementary reactions.
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NASA Astrophysics Data System (ADS)
Peng, Yan
2017-07-01
We study a general flat space/boson star transition model in quasi-local ensemble through approaches familiar from holographic superconductor theories. We manage to find a parameter ψ 2, which is proved to be useful in disclosing properties of phase transitions. In this work, we explore effects of the scalar mass, scalar charge and Stückelberg mechanism on the critical phase transition points and the order of transitions mainly from behaviors of the parameter ψ 2. We mention that properties of transitions in quasi-local gravity are strikingly similar to those in holographic superconductor models. We also obtain an analytical relation ψ 2 ∝ ( μ - μ c )1/2, which also holds for the condensed scalar operator in the holographic insulator/superconductor system in accordance with mean field theories.
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Foundations and latest advances in replica exchange transition interface sampling.
Cabriolu, Raffaela; Skjelbred Refsnes, Kristin M; Bolhuis, Peter G; van Erp, Titus S
2017-10-21
Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations.
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Foundations and latest advances in replica exchange transition interface sampling
NASA Astrophysics Data System (ADS)
Cabriolu, Raffaela; Skjelbred Refsnes, Kristin M.; Bolhuis, Peter G.; van Erp, Titus S.
2017-10-01
Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations.
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Phase diagram of two-dimensional hard ellipses.
Bautista-Carbajal, Gustavo; Odriozola, Gerardo
2014-05-28
We report the phase diagram of two-dimensional hard ellipses as obtained from replica exchange Monte Carlo simulations. The replica exchange is implemented by expanding the isobaric ensemble in pressure. The phase diagram shows four regions: isotropic, nematic, plastic, and solid (letting aside the hexatic phase at the isotropic-plastic two-step transition [E. P. Bernard and W. Krauth, Phys. Rev. Lett. 107, 155704 (2011)]). At low anisotropies, the isotropic fluid turns into a plastic phase which in turn yields a solid for increasing pressure (area fraction). Intermediate anisotropies lead to a single first order transition (isotropic-solid). Finally, large anisotropies yield an isotropic-nematic transition at low pressures and a high-pressure nematic-solid transition. We obtain continuous isotropic-nematic transitions. For the transitions involving quasi-long-range positional ordering, i.e., isotropic-plastic, isotropic-solid, and nematic-solid, we observe bimodal probability density functions. This supports first order transition scenarios.
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NASA Astrophysics Data System (ADS)
Neggers, R. A. J.; Ackerman, A. S.; Angevine, W. M.; Bazile, E.; Beau, I.; Blossey, P. N.; Boutle, I. A.; de Bruijn, C.; Cheng, A.; van der Dussen, J.; Fletcher, J.; Dal Gesso, S.; Jam, A.; Kawai, H.; Cheedela, S. K.; Larson, V. E.; Lefebvre, M.-P.; Lock, A. P.; Meyer, N. R.; de Roode, S. R.; de Rooy, W.; Sandu, I.; Xiao, H.; Xu, K.-M.
2017-10-01
Results are presented of the GASS/EUCLIPSE single-column model intercomparison study on the subtropical marine low-level cloud transition. A central goal is to establish the performance of state-of-the-art boundary-layer schemes for weather and climate models for this cloud regime, using large-eddy simulations of the same scenes as a reference. A novelty is that the comparison covers four different cases instead of one, in order to broaden the covered parameter space. Three cases are situated in the North-Eastern Pacific, while one reflects conditions in the North-Eastern Atlantic. A set of variables is considered that reflects key aspects of the transition process, making use of simple metrics to establish the model performance. Using this method, some longstanding problems in low-level cloud representation are identified. Considerable spread exists among models concerning the cloud amount, its vertical structure, and the associated impact on radiative transfer. The sign and amplitude of these biases differ somewhat per case, depending on how far the transition has progressed. After cloud breakup the ensemble median exhibits the well-known "too few too bright" problem. The boundary-layer deepening rate and its state of decoupling are both underestimated, while the representation of the thin capping cloud layer appears complicated by a lack of vertical resolution. Encouragingly, some models are successful in representing the full set of variables, in particular, the vertical structure and diurnal cycle of the cloud layer in transition. An intriguing result is that the median of the model ensemble performs best, inspiring a new approach in subgrid parameterization.
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NASA Astrophysics Data System (ADS)
Marsman, A.; Horbatsch, M.; Hessels, E. A.
2017-12-01
The resonant line shape from driving a transition between two states, |a 〉 and |b 〉 , can be distorted due to a quantum-mechanical interference effect involving a resonance between two different states, |c 〉 and |d 〉 , if |c 〉 has a decay path to |a 〉 and |d 〉 has a decay path to |b 〉 . This interference can cause a shift of the measured resonance, despite the fact that the two resonances do not have a common initial or final state. As an example, we demonstrate that such a shift affects measurements of the atomic hydrogen 2 S1 /2 -to-2 P1 /2 Lamb-shift transition due to 3 S -to-3 P transitions if the 3 S1 /2 state has some initial population.
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Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making
Seamans, Jeremy K.; Durstewitz, Daniel
2011-01-01
A common theoretical view is that attractor-like properties of neuronal dynamics underlie cognitive processing. However, although often proposed theoretically, direct experimental support for the convergence of neural activity to stable population patterns as a signature of attracting states has been sparse so far, especially in higher cortical areas. Combining state space reconstruction theorems and statistical learning techniques, we were able to resolve details of anterior cingulate cortex (ACC) multiple single-unit activity (MSUA) ensemble dynamics during a higher cognitive task which were not accessible previously. The approach worked by constructing high-dimensional state spaces from delays of the original single-unit firing rate variables and the interactions among them, which were then statistically analyzed using kernel methods. We observed cognitive-epoch-specific neural ensemble states in ACC which were stable across many trials (in the sense of being predictive) and depended on behavioral performance. More interestingly, attracting properties of these cognitively defined ensemble states became apparent in high-dimensional expansions of the MSUA spaces due to a proper unfolding of the neural activity flow, with properties common across different animals. These results therefore suggest that ACC networks may process different subcomponents of higher cognitive tasks by transiting among different attracting states. PMID:21625577
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NASA Technical Reports Server (NTRS)
Schobeiri, M. T.; Radke, R. E.
1996-01-01
Boundary layer transition and development on a turbomachinery blade is subjected to highly periodic unsteady turbulent flow, pressure gradient in longitudinal as well as lateral direction, and surface curvature. To study the effects of periodic unsteady wakes on the concave surface of a turbine blade, a curved plate was utilized. On the concave surface of this plate, detailed experimental investigations were carried out under zero and negative pressure gradient. The measurements were performed in an unsteady flow research facility using a rotating cascade of rods positioned upstream of the curved plate. Boundary layer measurements using a hot-wire probe were analyzed by the ensemble-averaging technique. The results presented in the temporal-spatial domain display the transition and further development of the boundary layer, specifically the ensemble-averaged velocity and turbulence intensity. As the results show, the turbulent patches generated by the wakes have different leading and trailing edge velocities and merge with the boundary layer resulting in a strong deformation and generation of a high turbulence intensity core. After the turbulent patch has totally penetrated into the boundary layer, pronounced becalmed regions were formed behind the turbulent patch and were extended far beyond the point they would occur in the corresponding undisturbed steady boundary layer.
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NASA Astrophysics Data System (ADS)
Wainwright, Carroll L.
2012-09-01
I present a numerical package (CosmoTransitions) for analyzing finite-temperature cosmological phase transitions driven by single or multiple scalar fields. The package analyzes the different vacua of a theory to determine their critical temperatures (where the vacuum energy levels are degenerate), their supercooling temperatures, and the bubble wall profiles which separate the phases and describe their tunneling dynamics. I introduce a new method of path deformation to find the profiles of both thin- and thick-walled bubbles. CosmoTransitions is freely available for public use.Program summaryProgram Title: CosmoTransitionsCatalogue identifier: AEML_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEML_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 8775No. of bytes in distributed program, including test data, etc.: 621096Distribution format: tar.gzProgramming language: Python.Computer: Developed on a 2009 MacBook Pro. No computer-specific optimization was performed.Operating system: Designed and tested on Mac OS X 10.6.8. Compatible with any OS with Python installed.RAM: Approximately 50 MB, mostly for loading plotting packages.Classification: 1.9, 11.1.External routines: SciPy, NumPy, matplotLibNature of problem: I describe a program to analyze early-Universe finite-temperature phase transitions with multiple scalar fields. The goal is to analyze the phase structure of an input theory, determine the amount of supercooling at each phase transition, and find the bubble-wall profiles of the nucleated bubbles that drive the transitions.Solution method: To find the bubble-wall profile, the program assumes that tunneling happens along a fixed path in field space. This reduces the equations of motion to one dimension, which can then be solved using the overshoot/undershoot method. The path iteratively deforms in the direction opposite the forces perpendicular to the path until the perpendicular forces vanish (or become very small). To find the phase structure, the program finds and integrates the change in a phase's minimum with respect to temperature.Running time: Approximately 1 minute for full analysis of the two-scalar-field test model on a 2.5 GHz CPU.
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NASA Astrophysics Data System (ADS)
Jin, Lingxia; Shi, Shengnan; Zhao, Yang; Luo, Liyang; Zhao, Caibin; Lu, Jiufu; Jiang, Min
2018-02-01
The direct tautomerism (path A) and H2O2 as a catalyst (path B) have been studied in conversion of Cyt2t+ into CytN3+ isomer. The protonated 5-carboxycytosine (5-caCyt) is represented and has been further explored in the presence of H2O2 (path C). In going from a four-membered-ring transition state in the case of the direct tautomerism to the six-membered ring for H2O2, the H2O2 significantly contributes to decreasing the free energy barrier of tautomerisation. Although the carboxylic substituent of 5-carboxycytosine has certain affected on the electron distribution of the pyrimidine ring, the six-membered-ring transition state has not changed. This result illustrates that the C5-carboxylation has no significant effect on the H2O2-mediated isomerisation of Cyt2t+ to CytN3+ isomer. Meanwhile, these paths A-C have been further explored in the presence of two water molecules. Use of implicit solvent models (PCM) does not significantly alter the energetics of water-mediated paths A-C compared to those in gas phase. Furthermore, the rate constant with Wigner tunnelling correction of path A is obviously smaller than those of paths B and C. Finally, the lifetime τ99.9% of paths B and C is 10-5 s, which is implemented by the mechanism of the concerted synchronous double proton transfer.
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Variational transition state theory: theoretical framework and recent developments.
Bao, Junwei Lucas; Truhlar, Donald G
2017-12-11
This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications. The theoretical methods reviewed here include multidimensional quantum mechanical tunneling, multistructural VTST (MS-VTST), multi-path VTST (MP-VTST), both reaction-path VTST (RP-VTST) and variable reaction coordinate VTST (VRC-VTST), system-specific quantum Rice-Ramsperger-Kassel theory (SS-QRRK) for predicting pressure-dependent rate constants, and VTST in the solid phase, liquid phase, and enzymes. We also provide some perspectives regarding the general applicability of VTST.
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Improving Upon String Methods for Transition State Discovery.
Chaffey-Millar, Hugh; Nikodem, Astrid; Matveev, Alexei V; Krüger, Sven; Rösch, Notker
2012-02-14
Transition state discovery via application of string methods has been researched on two fronts. The first front involves development of a new string method, named the Searching String method, while the second one aims at estimating transition states from a discretized reaction path. The Searching String method has been benchmarked against a number of previously existing string methods and the Nudged Elastic Band method. The developed methods have led to a reduction in the number of gradient calls required to optimize a transition state, as compared to existing methods. The Searching String method reported here places new beads on a reaction pathway at the midpoint between existing beads, such that the resolution of the path discretization in the region containing the transition state grows exponentially with the number of beads. This approach leads to favorable convergence behavior and generates more accurate estimates of transition states from which convergence to the final transition states occurs more readily. Several techniques for generating improved estimates of transition states from a converged string or nudged elastic band have been developed and benchmarked on 13 chemical test cases. Optimization approaches for string methods, and pitfalls therein, are discussed.
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Transition path theory analysis of c-Src kinase activation
Meng, Yilin; Shukla, Diwakar; Pande, Vijay S.; Roux, Benoît
2016-01-01
Nonreceptor tyrosine kinases of the Src family are large multidomain allosteric proteins that are crucial to cellular signaling pathways. In a previous study, we generated a Markov state model (MSM) to simulate the activation of c-Src catalytic domain, used as a prototypical tyrosine kinase. The long-time kinetics of transition predicted by the MSM was in agreement with experimental observations. In the present study, we apply the framework of transition path theory (TPT) to the previously constructed MSM to characterize the main features of the activation pathway. The analysis indicates that the activating transition, in which the activation loop first opens up followed by an inward rotation of the αC-helix, takes place via a dense set of intermediate microstates distributed within a fairly broad “transition tube” in a multidimensional conformational subspace connecting the two end-point conformations. Multiple microstates with negligible equilibrium probabilities carry a large transition flux associated with the activating transition, which explains why extensive conformational sampling is necessary to accurately determine the kinetics of activation. Our results suggest that the combination of MSM with TPT provides an effective framework to represent conformational transitions in complex biomolecular systems. PMID:27482115
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Ovis: A Framework for Visual Analysis of Ocean Forecast Ensembles.
Höllt, Thomas; Magdy, Ahmed; Zhan, Peng; Chen, Guoning; Gopalakrishnan, Ganesh; Hoteit, Ibrahim; Hansen, Charles D; Hadwiger, Markus
2014-08-01
We present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations of the sea surface height that is used in ocean forecasting. The position of eddies can be derived directly from the sea surface height and our visualization approach enables their interactive exploration and analysis.The behavior of eddies is important in different application settings of which we present two in this paper. First, we show an application for interactive planning of placement as well as operation of off-shore structures using real-world ensemble simulation data of the Gulf of Mexico. Off-shore structures, such as those used for oil exploration, are vulnerable to hazards caused by eddies, and the oil and gas industry relies on ocean forecasts for efficient operations. We enable analysis of the spatial domain, as well as the temporal evolution, for planning the placement and operation of structures.Eddies are also important for marine life. They transport water over large distances and with it also heat and other physical properties as well as biological organisms. In the second application we present the usefulness of our tool, which could be used for planning the paths of autonomous underwater vehicles, so called gliders, for marine scientists to study simulation data of the largely unexplored Red Sea.
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Nanoscale Electronic Conditioning for Improvement of Nanowire Light-Emitting-Diode Efficiency.
May, Brelon J; Belz, Matthew R; Ahamed, Arshad; Sarwar, A T M G; Selcu, Camelia M; Myers, Roberto C
2018-04-24
Commercial III-Nitride LEDs and lasers spanning visible and ultraviolet wavelengths are based on epitaxial films. Alternatively, nanowire-based III-Nitride optoelectronics offer the advantage of strain compliance and high crystalline quality growth on a variety of inexpensive substrates. However, nanowire LEDs exhibit an inherent property distribution, resulting in uneven current spreading through macroscopic devices that consist of millions of individual nanowire diodes connected in parallel. Despite being electrically connected, only a small fraction of nanowires, sometimes <1%, contribute to the electroluminescence (EL). Here, we show that a population of electrical shorts exists in the devices, consisting of a subset of low-resistance nanowires that pass a large portion of the total current in the ensemble devices. Burn-in electronic conditioning is performed by applying a short-term overload voltage; the nanoshorts experience very high current density, sufficient to render them open circuits, thereby forcing a new current path through more nanowire LEDs in an ensemble device. Current-voltage measurements of individual nanowires are acquired using conductive atomic force microscopy to observe the removal of nanoshorts using burn-in. In macroscopic devices, this results in a 33× increase in peak EL and reduced leakage current. Burn-in conditioning of nanowire ensembles therefore provides a straightforward method to mitigate nonuniformities inherent to nanowire devices.
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Quantum trajectory phase transitions in the micromaser.
Garrahan, Juan P; Armour, Andrew D; Lesanovsky, Igor
2011-08-01
We study the dynamics of the single-atom maser, or micromaser, by means of the recently introduced method of thermodynamics of quantum jump trajectories. We find that the dynamics of the micromaser displays multiple space-time phase transitions, i.e., phase transitions in ensembles of quantum jump trajectories. This rich dynamical phase structure becomes apparent when trajectories are classified by dynamical observables that quantify dynamical activity, such as the number of atoms that have changed state while traversing the cavity. The space-time transitions can be either first order or continuous, and are controlled not just by standard parameters of the micromaser but also by nonequilibrium "counting" fields. We discuss how the dynamical phase behavior relates to the better known stationary-state properties of the micromaser.
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Localization of soft modes at the depinning transition
NASA Astrophysics Data System (ADS)
Cao, Xiangyu; Bouzat, Sebastian; Kolton, Alejandro B.; Rosso, Alberto
2018-02-01
We characterize the soft modes of the dynamical matrix at the depinning transition, and compare the matrix with the properties of the Anderson model (and long-range generalizations). The density of states at the edge of the spectrum displays a universal linear tail, different from the Lifshitz tails. The eigenvectors are instead very similar in the two matrix ensembles. We focus on the ground state (soft mode), which represents the epicenter of avalanche instabilities. We expect it to be localized in all finite dimensions, and make a clear connection between its localization length and the Larkin length of the depinning model. In the fully connected model, we show that the weak-strong pinning transition coincides with a peculiar localization transition of the ground state.
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Superradiant phase transition in a model of three-level-Λ systems interacting with two bosonic modes
NASA Astrophysics Data System (ADS)
Hayn, Mathias; Emary, Clive; Brandes, Tobias
2012-12-01
We consider an ensemble of three-level particles in Lambda configuration interacting with two bosonic modes. The Hamiltonian has the form of a generalized Dicke model. We show that in the thermodynamic limit this model supports a superradiant quantum phase transition. Remarkably, this can be both a first- and a second-order phase transition. A connection of the phase diagram to the symmetries of the Hamiltonian is also given. In addition, we show that this model can describe atoms interacting with an electromagnetic field in which the microscopic Hamiltonian includes a diamagnetic contribution. Even though the parameters of the atomic system respect the Thomas-Reiche-Kuhn sum rule, the system still shows a superradiant phase transition.
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NASA Technical Reports Server (NTRS)
Crouch, Roger
2004-01-01
Viewgraphs on NASA's transition to its vision for space exploration is presented. The topics include: 1) Strategic Directives Guiding the Human Support Technology Program; 2) Progressive Capabilities; 3) A Journey to Inspire, Innovate, and Discover; 4) Risk Mitigation Status Technology Readiness Level (TRL) and Countermeasures Readiness Level (CRL); 5) Biological And Physical Research Enterprise Aligning With The Vision For U.S. Space Exploration; 6) Critical Path Roadmap Reference Missions; 7) Rating Risks; 8) Current Critical Path Roadmap (Draft) Rating Risks: Human Health; 9) Current Critical Path Roadmap (Draft) Rating Risks: System Performance/Efficiency; 10) Biological And Physical Research Enterprise Efforts to Align With Vision For U.S. Space Exploration; 11) Aligning with the Vision: Exploration Research Areas of Emphasis; 12) Code U Efforts To Align With The Vision For U.S. Space Exploration; 13) Types of Critical Path Roadmap Risks; and 14) ISS Human Support Systems Research, Development, and Demonstration. A summary discussing the vision for U.S. space exploration is also provided.
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Exploring the complexity of quantum control optimization trajectories.
Nanduri, Arun; Shir, Ofer M; Donovan, Ashley; Ho, Tak-San; Rabitz, Herschel
2015-01-07
The control of quantum system dynamics is generally performed by seeking a suitable applied field. The physical objective as a functional of the field forms the quantum control landscape, whose topology, under certain conditions, has been shown to contain no critical point suboptimal traps, thereby enabling effective searches for fields that give the global maximum of the objective. This paper addresses the structure of the landscape as a complement to topological critical point features. Recent work showed that landscape structure is highly favorable for optimization of state-to-state transition probabilities, in that gradient-based control trajectories to the global maximum value are nearly straight paths. The landscape structure is codified in the metric R ≥ 1.0, defined as the ratio of the length of the control trajectory to the Euclidean distance between the initial and optimal controls. A value of R = 1 would indicate an exactly straight trajectory to the optimal observable value. This paper extends the state-to-state transition probability results to the quantum ensemble and unitary transformation control landscapes. Again, nearly straight trajectories predominate, and we demonstrate that R can take values approaching 1.0 with high precision. However, the interplay of optimization trajectories with critical saddle submanifolds is found to influence landscape structure. A fundamental relationship necessary for perfectly straight gradient-based control trajectories is derived, wherein the gradient on the quantum control landscape must be an eigenfunction of the Hessian. This relation is an indicator of landscape structure and may provide a means to identify physical conditions when control trajectories can achieve perfect linearity. The collective favorable landscape topology and structure provide a foundation to understand why optimal quantum control can be readily achieved.
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Frictional behaviour of sandstone: A sample-size dependent triaxial investigation
NASA Astrophysics Data System (ADS)
Roshan, Hamid; Masoumi, Hossein; Regenauer-Lieb, Klaus
2017-01-01
Frictional behaviour of rocks from the initial stage of loading to final shear displacement along the formed shear plane has been widely investigated in the past. However the effect of sample size on such frictional behaviour has not attracted much attention. This is mainly related to the limitations in rock testing facilities as well as the complex mechanisms involved in sample-size dependent frictional behaviour of rocks. In this study, a suite of advanced triaxial experiments was performed on Gosford sandstone samples at different sizes and confining pressures. The post-peak response of the rock along the formed shear plane has been captured for the analysis with particular interest in sample-size dependency. Several important phenomena have been observed from the results of this study: a) the rate of transition from brittleness to ductility in rock is sample-size dependent where the relatively smaller samples showed faster transition toward ductility at any confining pressure; b) the sample size influences the angle of formed shear band and c) the friction coefficient of the formed shear plane is sample-size dependent where the relatively smaller sample exhibits lower friction coefficient compared to larger samples. We interpret our results in terms of a thermodynamics approach in which the frictional properties for finite deformation are viewed as encompassing a multitude of ephemeral slipping surfaces prior to the formation of the through going fracture. The final fracture itself is seen as a result of the self-organisation of a sufficiently large ensemble of micro-slip surfaces and therefore consistent in terms of the theory of thermodynamics. This assumption vindicates the use of classical rock mechanics experiments to constrain failure of pressure sensitive rocks and the future imaging of these micro-slips opens an exciting path for research in rock failure mechanisms.
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International Space Station: Transitional Platform for Moon and Mars
NASA Technical Reports Server (NTRS)
Greeniesen, Michael C.
2006-01-01
Humans on the path to Mars are employing the Space Station to better understand the Life Sciences issues during long duration space flight. In this phase the problems, for example, of bone loss, skeletal muscle atrophy and radiation will be prioritized for countermeasure development. This presentation will feature NASA's critical path to the Moon and Mars as the initial blueprint for addressing these Human Life Sciences challenges necessary to accomplish a successful Mars transit, surface exploration and return to Earth. A Moon base will be the test bed for resolving the engineering obstacles for later establishment of the Mars Crew Habitat. Current engineering concept scenarios for Moon and Mars bases plus Mars transit vehicles will receive the final focus.
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The Influence of Internal Model Variability in GEOS-5 on Interhemispheric CO2 Exchange
NASA Technical Reports Server (NTRS)
Allen, Melissa; Erickson, David; Kendall, Wesley; Fu, Joshua; Ott, Leslie; Pawson, Steven
2012-01-01
An ensemble of eight atmospheric CO2 simulations was completed employing the National Aeronautics and Space Administration (NASA) Goddard Earth Observation System, Version 5 (GEOS-5) for the years 2000-2001, each with initial meteorological conditions corresponding to different days in January 2000 to examine internal model variability. Globally, the model runs show similar concentrations of CO2 for the two years, but in regions of high CO2 concentrations due to fossil fuel emissions, large differences among different model simulations appear. The phasing and amplitude of the CO2 cycle at Northern Hemisphere locations in all of the ensemble members is similar to that of surface observations. In several southern hemisphere locations, however, some of the GEOS-5 model CO2 cycles are out of phase by as much as four months, and large variations occur between the ensemble members. This result indicates that there is large sensitivity to transport in these regions. The differences vary by latitude-the most extreme differences in the Tropics and the least at the South Pole. Examples of these differences among the ensemble members with regard to CO2 uptake and respiration of the terrestrial biosphere and CO2 emissions due to fossil fuel emissions are shown at Cape Grim, Tasmania. Integration-based flow analysis of the atmospheric circulation in the model runs shows widely varying paths of flow into the Tasmania region among the models including sources from North America, South America, South Africa, South Asia and Indonesia. These results suggest that interhemispheric transport can be strongly influenced by internal model variability.
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Relation Between Pore Size and the Compressibility of a Confined Fluid
Gor, Gennady Y.; Siderius, Daniel W.; Rasmussen, Christopher J.; Krekelberg, William P.; Shen, Vincent K.; Bernstein, Noam
2015-01-01
When a fluid is confined to a nanopore, its thermodynamic properties differ from the properties of a bulk fluid, so measuring such properties of the confined fluid can provide information about the pore sizes. Here we report a simple relation between the pore size and isothermal compressibility of argon confined in these pores. Compressibility is calculated from the fluctuations of the number of particles in the grand canonical ensemble using two different simulation techniques: conventional grand-canonical Monte Carlo and grand-canonical ensemble transition-matrix Monte Carlo. Our results provide a theoretical framework for extracting the information on the pore sizes of fluid-saturated samples by measuring the compressibility from ultrasonic experiments. PMID:26590541
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Continuous Easy-Plane Deconfined Phase Transition on the Kagome Lattice
NASA Astrophysics Data System (ADS)
Zhang, Xue-Feng; He, Yin-Chen; Eggert, Sebastian; Moessner, Roderich; Pollmann, Frank
2018-03-01
We use large scale quantum Monte Carlo simulations to study an extended Hubbard model of hard core bosons on the kagome lattice. In the limit of strong nearest-neighbor interactions at 1 /3 filling, the interplay between frustration and quantum fluctuations leads to a valence bond solid ground state. The system undergoes a quantum phase transition to a superfluid phase as the interaction strength is decreased. It is still under debate whether the transition is weakly first order or represents an unconventional continuous phase transition. We present a theory in terms of an easy plane noncompact C P1 gauge theory describing the phase transition at 1 /3 filling. Utilizing large scale quantum Monte Carlo simulations with parallel tempering in the canonical ensemble up to 15552 spins, we provide evidence that the phase transition is continuous at exactly 1 /3 filling. A careful finite size scaling analysis reveals an unconventional scaling behavior hinting at deconfined quantum criticality.
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Thermodynamics and glassy phase transition of regular black holes
NASA Astrophysics Data System (ADS)
Javed, Wajiha; Yousaf, Z.; Akhtar, Zunaira
2018-05-01
This paper is aimed to study thermodynamical properties of phase transition for regular charged black holes (BHs). In this context, we have considered two different forms of BH metrics supplemented with exponential and logistic distribution functions and investigated the recent expansion of phase transition through grand canonical ensemble. After exploring the corresponding Ehrenfest’s equation, we found the second-order background of phase transition at critical points. In order to check the critical behavior of regular BHs, we have evaluated some corresponding explicit relations for the critical temperature, pressure and volume and draw certain graphs with constant values of Smarr’s mass. We found that for the BH metric with exponential configuration function, the phase transition curves are divergent near the critical points, while glassy phase transition has been observed for the Ayón-Beato-García-Bronnikov (ABGB) BH in n = 5 dimensions.
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Frank, Joachim; Gonzalez, Ruben L.
2015-01-01
At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describes transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy and single-molecule fluorescence resonance energy transfer studies of the bacterial ribosomal pretranslocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pretranslocation complex, which are observed in a cryogenic electron microscopy study, may not be observed in several single-molecule fluorescence resonance energy transfer studies. PMID:25785884
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Statistical mechanics framework for static granular matter.
Henkes, Silke; Chakraborty, Bulbul
2009-06-01
The physical properties of granular materials have been extensively studied in recent years. So far, however, there exists no theoretical framework which can explain the observations in a unified manner beyond the phenomenological jamming diagram. This work focuses on the case of static granular matter, where we have constructed a statistical ensemble which mirrors equilibrium statistical mechanics. This ensemble, which is based on the conservation properties of the stress tensor, is distinct from the original Edwards ensemble and applies to packings of deformable grains. We combine it with a field theoretical analysis of the packings, where the field is the Airy stress function derived from the force and torque balance conditions. In this framework, Point J characterized by a diverging stiffness of the pressure fluctuations. Separately, we present a phenomenological mean-field theory of the jamming transition, which incorporates the mean contact number as a variable. We link both approaches in the context of the marginal rigidity picture proposed by Wyart and others.
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Thompson, Colin D Kinz; Sharma, Ajeet K; Frank, Joachim; Gonzalez, Ruben L; Chowdhury, Debashish
2015-08-27
At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describe transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies of the bacterial ribosomal pre-translocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pre-translocation complex, which are observed in a cryo-EM study, may not be observed in several smFRET studies.
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Theory of the vortex-clustering transition in a confined two-dimensional quantum fluid
NASA Astrophysics Data System (ADS)
Yu, Xiaoquan; Billam, Thomas P.; Nian, Jun; Reeves, Matthew T.; Bradley, Ashton S.
2016-08-01
Clustering of like-sign vortices in a planar bounded domain is known to occur at negative temperature, a phenomenon that Onsager demonstrated to be a consequence of bounded phase space. In a confined superfluid, quantized vortices can support such an ordered phase, provided they evolve as an almost isolated subsystem containing sufficient energy. A detailed theoretical understanding of the statistical mechanics of such states thus requires a microcanonical approach. Here we develop an analytical theory of the vortex clustering transition in a neutral system of quantum vortices confined to a two-dimensional disk geometry, within the microcanonical ensemble. The choice of ensemble is essential for identifying the correct thermodynamic limit of the system, enabling a rigorous description of clustering in the language of critical phenomena. As the system energy increases above a critical value, the system develops global order via the emergence of a macroscopic dipole structure from the homogeneous phase of vortices, spontaneously breaking the Z2 symmetry associated with invariance under vortex circulation exchange, and the rotational SO (2 ) symmetry due to the disk geometry. The dipole structure emerges characterized by the continuous growth of the macroscopic dipole moment which serves as a global order parameter, resembling a continuous phase transition. The critical temperature of the transition, and the critical exponent associated with the dipole moment, are obtained exactly within mean-field theory. The clustering transition is shown to be distinct from the final state reached at high energy, known as supercondensation. The dipole moment develops via two macroscopic vortex clusters and the cluster locations are found analytically, both near the clustering transition and in the supercondensation limit. The microcanonical theory shows excellent agreement with Monte Carlo simulations, and signatures of the transition are apparent even for a modest system of 100 vortices, accessible in current Bose-Einstein condensate experiments.
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de Guglielmo, Giordano; Crawford, Elena; Kim, Sarah; Vendruscolo, Leandro F; Hope, Bruce T; Brennan, Molly; Cole, Maury; Koob, George F; George, Olivier
2016-09-07
Abstinence from alcohol is associated with the recruitment of neurons in the central nucleus of the amygdala (CeA) in nondependent rats that binge drink alcohol and in alcohol-dependent rats. However, whether the recruitment of this neuronal ensemble in the CeA is causally related to excessive alcohol drinking or if it represents a consequence of excessive drinking remains unknown. We tested the hypothesis that the recruitment of a neuronal ensemble in the CeA during abstinence is required for excessive alcohol drinking in nondependent rats that binge drink alcohol and in alcohol-dependent rats. We found that inactivation of the CeA neuronal ensemble during abstinence significantly decreased alcohol drinking in both groups. In nondependent rats, the decrease in alcohol intake was transient and returned to normal the day after the injection. In dependent rats, inactivation of the neuronal ensemble with Daun02 produced a long-term decrease in alcohol drinking. Moreover, we observed a significant reduction of somatic withdrawal signs in dependent animals that were injected with Daun02 in the CeA. These results indicate that the recruitment of a neuronal ensemble in the CeA during abstinence from alcohol is causally related to excessive alcohol drinking in alcohol-dependent rats, whereas a similar neuronal ensemble only partially contributed to alcohol-binge-like drinking in nondependent rats. These results identify a critical neurobiological mechanism that may be required for the transition to alcohol dependence, suggesting that focusing on the neuronal ensemble in the CeA may lead to a better understanding of the etiology of alcohol use disorders and improve medication development. Alcohol dependence recruits neurons in the central nucleus of the amygdala (CeA). Here, we found that inactivation of a specific dependence-induced neuronal ensemble in the CeA reversed excessive alcohol drinking and somatic signs of alcohol dependence in rats. These results identify a critical neurobiological mechanism that is required for alcohol dependence, suggesting that targeting dependence neuronal ensembles may lead to a better understanding of the etiology of alcohol use disorders, with implications for diagnosis, prevention, and treatment. Copyright © 2016 the authors 0270-6474/16/369446-08$15.00/0.
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An inhibitory gate for state transition in cortex
Zucca, Stefano; D’Urso, Giulia; Pasquale, Valentina; Vecchia, Dania; Pica, Giuseppe; Bovetti, Serena; Moretti, Claudio; Varani, Stefano; Molano-Mazón, Manuel; Chiappalone, Michela; Panzeri, Stefano; Fellin, Tommaso
2017-01-01
Large scale transitions between active (up) and silent (down) states during quiet wakefulness or NREM sleep regulate fundamental cortical functions and are known to involve both excitatory and inhibitory cells. However, if and how inhibition regulates these activity transitions is unclear. Using fluorescence-targeted electrophysiological recording and cell-specific optogenetic manipulation in both anesthetized and non-anesthetized mice, we found that two major classes of interneurons, the parvalbumin and the somatostatin positive cells, tightly control both up-to-down and down-to-up state transitions. Inhibitory regulation of state transition was observed under both natural and optogenetically-evoked conditions. Moreover, perturbative optogenetic experiments revealed that the inhibitory control of state transition was interneuron-type specific. Finally, local manipulation of small ensembles of interneurons affected cortical populations millimetres away from the modulated region. Together, these results demonstrate that inhibition potently gates transitions between cortical activity states, and reveal the cellular mechanisms by which local inhibitory microcircuits regulate state transitions at the mesoscale. DOI: http://dx.doi.org/10.7554/eLife.26177.001 PMID:28509666
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Stationary properties of maximum-entropy random walks.
Dixit, Purushottam D
2015-10-01
Maximum-entropy (ME) inference of state probabilities using state-dependent constraints is popular in the study of complex systems. In stochastic systems, how state space topology and path-dependent constraints affect ME-inferred state probabilities remains unknown. To that end, we derive the transition probabilities and the stationary distribution of a maximum path entropy Markov process subject to state- and path-dependent constraints. A main finding is that the stationary distribution over states differs significantly from the Boltzmann distribution and reflects a competition between path multiplicity and imposed constraints. We illustrate our results with particle diffusion on a two-dimensional landscape. Connections with the path integral approach to diffusion are discussed.
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Radiative recombination in GaN/InGaN heterojunction bipolar transistors
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kao, Tsung-Ting; Lee, Yi-Che; Kim, Hee-Jin
2015-12-14
We report an electroluminescence (EL) study on npn GaN/InGaN heterojunction bipolar transistors (HBTs). Three radiative recombination paths are resolved in the HBTs, corresponding to the band-to-band transition (3.3 eV), conduction-band-to-acceptor-level transition (3.15 eV), and yellow luminescence (YL) with the emission peak at 2.2 eV. We further study possible light emission paths by operating the HBTs under different biasing conditions. The band-to-band and the conduction-band-to-acceptor-level transitions mostly arise from the intrinsic base region, while a defect-related YL band could likely originate from the quasi-neutral base region of a GaN/InGaN HBT. The I{sub B}-dependent EL intensities for these three recombination paths are discussed. The resultsmore » also show the radiative emission under the forward-active transistor mode operation is more effective than that using a diode-based emitter due to the enhanced excess electron concentration in the base region as increasing the collector current increases.« less
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Complex catalysts from self-repairing ensembles to highly reactive air-based oxidation systems
Craig L. Hill; Laurent Delannoy; Dean C. Duncan; Ira A. Weinstock; Roman F. Renneke; Richard S. Reiner; Rajai H. Atalla; Jong Woo Han; Daniel A. Hillesheim; Rui Cao; Travis M. Anderson; Nelya M. Okun; Djamaladdin G. Musaev; Yurii V. Geletii
2007-01-01
Progress in four interrelated catalysis research efforts in our laboratory are summarized: (1) catalytic photochemical functionalization of unactivated CeH bonds by polyoxometalates (POMs); (2) self-repairing catalysts; (3) catalysts for air-based oxidations under ambient conditions; and (4) terminal oxo complexes of the late-transition metal elements and their...
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Random center vortex lines in continuous 3D space-time
DOE Office of Scientific and Technical Information (OSTI.GOV)
Höllwieser, Roman; Institute of Atomic and Subatomic Physics, Vienna University of Technology, Operngasse 9, 1040 Vienna; Altarawneh, Derar
2016-01-22
We present a model of center vortices, represented by closed random lines in continuous 2+1-dimensional space-time. These random lines are modeled as being piece-wise linear and an ensemble is generated by Monte Carlo methods. The physical space in which the vortex lines are defined is a cuboid with periodic boundary conditions. Besides moving, growing and shrinking of the vortex configuration, also reconnections are allowed. Our ensemble therefore contains not a fixed, but a variable number of closed vortex lines. This is expected to be important for realizing the deconfining phase transition. Using the model, we study both vortex percolation andmore » the potential V(R) between quark and anti-quark as a function of distance R at different vortex densities, vortex segment lengths, reconnection conditions and at different temperatures. We have found three deconfinement phase transitions, as a function of density, as a function of vortex segment length, and as a function of temperature. The model reproduces the qualitative features of confinement physics seen in SU(2) Yang-Mills theory.« less
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NASA Astrophysics Data System (ADS)
Thorne, Robert; Keedy, Daniel; Warkentin, Matthew; Fraser, James; Moreau, David; Atakisi, Hakan; Rau, Peter
Proteins populate complex, temperature-dependent ensembles of conformations that enable their function. Yet in X-ray crystallographic studies, roughly 98% of structures have been determined at 100 K, and most refined to only a single conformation. A combination of experimental methods enabled by studies of ice formation and computational methods for mining low-density features in electron density maps have been applied to determine the evolution of the conformational landscapes of the enzymes cyclophilin A and urease between 300 K and 100 K. Minority conformations of most side chains depopulate on cooling from 300 to ~200 K, below which subsequent conformational evolution is quenched. The characteristic temperatures for this depopulation are highly heterogeneous throughout each enzyme. The temperature-dependent ensemble of the active site flap in urease has also been mapped. These all-atom, site-resolved measurements and analyses rule out one interpretation of the protein-solvent glass transition, and give an alternative interpretation of a dynamical transition identified in site-averaged experiments. They demonstrate a powerful approach to structural characterization of the dynamic underpinnings of protein function. Supported by NSF MCB-1330685.
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Brox, Dominik; Kiel, Alexander; Wörner, Svenja Johanna; Pernpointner, Markus; Comba, Peter; Martin, Bodo; Herten, Dirk-Peter
2013-01-01
Beyond their use in analytical chemistry fluorescent probes continuously gain importance because of recent applications of single-molecule fluorescence spectroscopy to monitor elementary reaction steps. In this context, we characterized quenching of a fluorescent probe by different metal ions with fluorescence spectroscopy in the bulk and at the single-molecule level. We apply a quantitative model to explain deviations from existing standard models for fluorescence quenching. The model is based on a reversible transition from a bright to a dim state upon binding of the metal ion. We use the model to estimate the stability constants of complexes with different metal ions and the change of the relative quantum yield of different reporter dye labels. We found ensemble data to agree widely with results from single-molecule experiments. Our data indicates a mechanism involving close molecular contact of dye and quenching moiety which we also found in molecular dynamics simulations. We close the manuscript with a discussion of possible mechanisms based on Förster distances and electrochemical potentials which renders photo-induced electron transfer to be more likely than Förster resonance energy transfer. PMID:23483966
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Smith, Kyle K G; Poulsen, Jens Aage; Nyman, Gunnar; Rossky, Peter J
2015-06-28
We develop two classes of quasi-classical dynamics that are shown to conserve the initial quantum ensemble when used in combination with the Feynman-Kleinert approximation of the density operator. These dynamics are used to improve the Feynman-Kleinert implementation of the classical Wigner approximation for the evaluation of quantum time correlation functions known as Feynman-Kleinert linearized path-integral. As shown, both classes of dynamics are able to recover the exact classical and high temperature limits of the quantum time correlation function, while a subset is able to recover the exact harmonic limit. A comparison of the approximate quantum time correlation functions obtained from both classes of dynamics is made with the exact results for the challenging model problems of the quartic and double-well potentials. It is found that these dynamics provide a great improvement over the classical Wigner approximation, in which purely classical dynamics are used. In a special case, our first method becomes identical to centroid molecular dynamics.
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Unimodular lattice triangulations as small-world and scale-free random graphs
NASA Astrophysics Data System (ADS)
Krüger, B.; Schmidt, E. M.; Mecke, K.
2015-02-01
Real-world networks, e.g., the social relations or world-wide-web graphs, exhibit both small-world and scale-free behaviour. We interpret lattice triangulations as planar graphs by identifying triangulation vertices with graph nodes and one-dimensional simplices with edges. Since these triangulations are ergodic with respect to a certain Pachner flip, applying different Monte Carlo simulations enables us to calculate average properties of random triangulations, as well as canonical ensemble averages, using an energy functional that is approximately the variance of the degree distribution. All considered triangulations have clustering coefficients comparable with real-world graphs; for the canonical ensemble there are inverse temperatures with small shortest path length independent of system size. Tuning the inverse temperature to a quasi-critical value leads to an indication of scale-free behaviour for degrees k≥slant 5. Using triangulations as a random graph model can improve the understanding of real-world networks, especially if the actual distance of the embedded nodes becomes important.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Neggers, R. A. J.; Ackerman, A. S.; Angevine, W. M.
Results are presented of the GASS/EUCLIPSE single-column model inter-comparison study on the subtropical marine low-level cloud transition. A central goal is to establish the performance of state-of-the-art boundary-layer schemes for weather and climate mod- els for this cloud regime, using large-eddy simulations of the same scenes as a reference. A novelty is that the comparison covers four different cases instead of one, in order to broaden the covered parameter space. Three cases are situated in the North-Eastern Pa- cific, while one reflects conditions in the North-Eastern Atlantic. A set of variables is considered that reflects key aspects of the transitionmore » process, making use of simple met- rics to establish the model performance. Using this method some longstanding problems in low level cloud representation are identified. Considerable spread exists among models concerning the cloud amount, its vertical structure and the associated impact on radia- tive transfer. The sign and amplitude of these biases differ somewhat per case, depending on how far the transition has progressed. After cloud breakup the ensemble median ex- hibits the well-known “too few too bright” problem. The boundary layer deepening rate and its state of decoupling are both underestimated, while the representation of the thin capping cloud layer appears complicated by a lack of vertical resolution. Encouragingly, some models are successful in representing the full set of variables, in particular the verti- cal structure and diurnal cycle of the cloud layer in transition. An intriguing result is that the median of the model ensemble performs best, inspiring a new approach in subgrid pa- rameterization.« less
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The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier
NASA Astrophysics Data System (ADS)
Lei, Hongxing; Deng, Xiaojian; Wang, Zhixiang; Duan, Yong
2008-10-01
The LYS24/29NLE double mutant of villin headpiece subdomain (HP35) is the fastest folding protein known so far with a folding time constant of 0.6μs. In this work, the folding mechanism of the mutant has been investigated by both conventional and replica exchange molecular dynamics (CMD and REMD) simulations with AMBER FF03 force field and a generalized-Born solvation model. Direct comparison to the ab initio folding of the wild type HP35 enabled a close examination on the mutational effect on the folding process. The mutant folded to the native state, as demonstrated by the 0.50Å Cα-root mean square deviation (RMSD) sampled in both CMD and REMD simulations and the high population of the folded conformation compared with the denatured conformations. Consistent with experiments, the significantly reduced primary folding free energy barrier makes the mutant closer to a downhill folder than the wild type HP35 that directly leads to the faster transition and higher melting temperature. However, unlike the proposed downhill folding which envisages a smooth shift between unfolded and folded states without transition barrier, we observed a well-defined folding transition that was consistent with experiments. Further examination of the secondary structures revealed that the two mutated residues have higher intrinsic helical preference that facilitated the formation of both helix III and the intermediate state which contains the folded segment helix II/III. Other factors contributing to the faster folding include the more favorable electrostatic interactions in the transition state with the removal of the charged NH3+ groups from LYS. In addition, both transition state ensemble and denatured state ensemble are shifted in the mutant.
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Quantum quench in an atomic one-dimensional Ising chain.
Meinert, F; Mark, M J; Kirilov, E; Lauber, K; Weinmann, P; Daley, A J; Nägerl, H-C
2013-08-02
We study nonequilibrium dynamics for an ensemble of tilted one-dimensional atomic Bose-Hubbard chains after a sudden quench to the vicinity of the transition point of the Ising paramagnetic to antiferromagnetic quantum phase transition. The quench results in coherent oscillations for the orientation of effective Ising spins, detected via oscillations in the number of doubly occupied lattice sites. We characterize the quench by varying the system parameters. We report significant modification of the tunneling rate induced by interactions and show clear evidence for collective effects in the oscillatory response.
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Rectification of Spatial Disorder
NASA Astrophysics Data System (ADS)
Um, Jaegon; Hong, Hyunsuk; Marchesoni, Fabio; Park, Hyunggyu
2012-02-01
We demonstrate that a large ensemble of noiseless globally coupled-pinned oscillators is capable of rectifying spatial disorder with spontaneous current activated through a dynamical phase transition mechanism, either of first or second order, depending on the profile of the pinning potential. In the presence of an external weak drive, the same collective mechanism can result in an absolute negative mobility, which, though not immediately related to symmetry breaking, is most prominent at the phase transition. Our results apply to a tug-of-war by competing molecular motors for bidirectional cargo transport.
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A short-term ensemble wind speed forecasting system for wind power applications
NASA Astrophysics Data System (ADS)
Baidya Roy, S.; Traiteur, J. J.; Callicutt, D.; Smith, M.
2011-12-01
This study develops an adaptive, blended forecasting system to provide accurate wind speed forecasts 1 hour ahead of time for wind power applications. The system consists of an ensemble of 21 forecasts with different configurations of the Weather Research and Forecasting Single Column Model (WRFSCM) and a persistence model. The ensemble is calibrated against observations for a 2 month period (June-July, 2008) at a potential wind farm site in Illinois using the Bayesian Model Averaging (BMA) technique. The forecasting system is evaluated against observations for August 2008 at the same site. The calibrated ensemble forecasts significantly outperform the forecasts from the uncalibrated ensemble while significantly reducing forecast uncertainty under all environmental stability conditions. The system also generates significantly better forecasts than persistence, autoregressive (AR) and autoregressive moving average (ARMA) models during the morning transition and the diurnal convective regimes. This forecasting system is computationally more efficient than traditional numerical weather prediction models and can generate a calibrated forecast, including model runs and calibration, in approximately 1 minute. Currently, hour-ahead wind speed forecasts are almost exclusively produced using statistical models. However, numerical models have several distinct advantages over statistical models including the potential to provide turbulence forecasts. Hence, there is an urgent need to explore the role of numerical models in short-term wind speed forecasting. This work is a step in that direction and is likely to trigger a debate within the wind speed forecasting community.
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Yamazaki, Kaoru; Niitsu, Naoyuki; Nakamura, Kosuke; Kanno, Manabu; Kono, Hirohiko
2012-11-26
We investigated the reaction paths of Stone-Wales rearrangement (SWR), i.e., π/2 rotation of two carbon atoms with respect to the midpoint of the bond, in graphene and carbon nanotube quantum chemically. Our particular attention is focused on the roles of electronic excitations and conical intersections (CIs) in the reaction mechanism. We used pyrene as a model system. The reaction paths were determined by constructing potential energy surfaces at the MS-CASPT2//SA-CASSCF level of theory. We found that there are no CIs involved in SWR when both of C-C bond cleavage and formation occur simultaneously (concerted mechanism). In contrast, for the reaction path with stepwise cleavage and formation of C-C bonds, C-C bond breaking and making processes proceed through two CIs. When SWR starts from the ground (S(0)) state, the concerted and stepwise paths have an equivalent reaction barrier ΔE(‡) (9.5-9.6 eV). For the reaction path starting from excited states, only the stepwise mechanism is energetically preferable. This path contains a nonadabatic transition between the S(1) and S(0) states via a CI associated with the first stage of C-C bond cleavage and has ΔE(‡) as large as in the S(0) paths. We confirmed that the main active molecular orbitals and electron configurations for the low-lying electronic states of larger nanocarbons are the same as those in pyrene. This result suggests the importance of the nonadiabatic transitions through CIs in the photochemical reactions in large nanocarbons.
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NASA Astrophysics Data System (ADS)
Janicka, Lucja; Szczepanik, Dominika; Borek, Karolina; Heese, Birgit; Stachlewska, Iwona S.
2018-04-01
The aerosol layers of different origin, suspended in the atmosphere on 9-11 August 2015 were observed with the PollyXT-UW lidar in Warsaw, Poland. The HYSPLIT ensemble backward trajectories indicate that the observed air-masses attribute to a few different sources, among others, possible transport paths from Ukraine, Slovakia, and Africa. In this paper, we attempt to analyse and discuss the properties of aerosol particles of different origin that were suspended over Warsaw during this event.
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NASA Astrophysics Data System (ADS)
Jarboe, N. A.; Coe, R. S.; Glen, J. M.; Paul, R. R.
2007-05-01
The best known record of the earth's magnetic field behavior during a geomagnetic polarity reversal preserved in volcanic rock is the reverse to normal (R-N) polarity reversal found in the Steens Basalts of SE Oregon. At three locations where reverse to normal sections are found (Steens Mountain, Catlow Peak, and Poker Jim Ridge), four high precision 40Ar/39Ar plateau ages of plagioclase separates from transitionally magnetized rocks were determined. The ages are the same within error and have a weighted mean age of 16.58 ± 0.14 Ma. Errors are two sigma. A more precise constraint on the youngest possible age of the reversal is 16.548 ± 0.050 Ma determined from the normally magnetized Oregon Canyon tuff capping the Catlow Peak section. Comparison of these ages to the new geomagnetic polarity time scale of Gradstein et al. (A Geologic Time Scale 2004, 589 pp., Cambridge University Press, 2004.), after adjustments due to differences in Fish Canyon sanidine (FCs) standard ages (28.02 Ma, this study; 28.24 Ma, Gradstein et al.), shows that the Steens reversal is uniquely identified as the top of the C5Cr chron. The high precision of the ages and the Steens' reversal location in the geomagnetic polarity timescale convincingly demonstrate that these stratigraphically uncorrelated transitional sections were erupted during the same transition and their transitional paths should be combined. The high-quality, detailed benchmark record of this reversal (Mankinen et al., JGR, 90(B), 10.393-10.416, 1985; Prevot et al., Nature, 316, 230-234, 1985) is a composite derived from two sampled sections 2 km apart on Steens Mountain that overlapped significantly, Steens A above and Steens B below. This study showed that the magnetic field during the reversal moved from reverse to normal and then bounced back to transitional before finally returning to normal (a R-T-N-T-N path). The unexamined upper part of the Steens B section was later sampled and revealed an additional bounce of the field during the transition (Camps et al., JGR, 104(B8), 17747- 58, 1999). This increased the reversal's complexity to a R-T-N-T-N-T-N pattern. We have studied a R-N volcanic section at Catlow Peak 70 km SSE of Steens Mountain with 32 flows erupted during the transition. The transitional directions trace a path very close to the Steens A and B reversal path but contain an additional large swing through the reversed field direction, demonstrating an even more complex R-T-N-T-N-T-R-T-N path. We will also report on two R-N sections recently sampled at Poker Jim Ridge 80 km west of Steens Mountain that add new directions to the Steens record. The complex composite Steens reversal path recorded in these high fidelity lavas gives some credence to suggestions of very complex magnetic field behavior during reversals, previously seen only in sediment records where the acquisition of magnetization is less well understood.
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Ultrafast electron crystallography of the cooperative reaction path in vanadium dioxide
Yang, Ding-Shyue; Baum, Peter; Zewail, Ahmed H.
2016-01-01
Time-resolved electron diffraction with atomic-scale spatial and temporal resolution was used to unravel the transformation pathway in the photoinduced structural phase transition of vanadium dioxide. Results from bulk crystals and single-crystalline thin-films reveal a common, stepwise mechanism: First, there is a femtosecond V−V bond dilation within 300 fs, second, an intracell adjustment in picoseconds and, third, a nanoscale shear motion within tens of picoseconds. Experiments at different ambient temperatures and pump laser fluences reveal a temperature-dependent excitation threshold required to trigger the transitional reaction path of the atomic motions. PMID:27376103
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A clock transition in a solid-state system
NASA Astrophysics Data System (ADS)
Edge, G. J. A.; Potnis, S.; Vutha, A. C.
2017-04-01
With the impending redefinition of the SI second based on optical frequency standards, new secondary frequency standards are needed in order to form clock ensembles. Ideally such secondary standards will offer enhanced robustness, portability and high signal-to-noise ratios (SNR), to enable rapid and precise comparisons to be made against primary standards. A clock based on a narrow optical transition, in atoms that are doped into a solid-state host, offers the experimental simplicity and large SNR to satisfy these requirements. The intra-configuration 7F0 ->5D0 transition, in Sm2+ ions doped into a host crystal, is an attractive candidate for such secondary standards due to its low susceptibility to perturbations from the crystal environment. We present results from the interrogation of this clock transition with a narrow linewidth laser.
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NASA Astrophysics Data System (ADS)
Kasper, David; Cole, Jackson L.; Gardner, Cristilyn N.; Garver, Bethany; Jarka, Kyla L.; Kar, Aman; McGough, Aylin M.; PeQueen, David J.; Rivera, Daniel Ivan; Jang-Condell, Hannah; Kobulnicky, Henry A.; Dale, Daniel A.
2018-06-01
We present new multi-broadband transit photometry of HD 189733b observed with the Wyoming Infrared Observatory. With an ensemble of Sloan filter observations across multiple transits we have created an ultra-low resolution transmission spectrum to discern the nature of the exoplanet atmosphere. This data set exemplifies the capabilities of the 2.3 m observatory. The analysis was performed with a Markov-Chain Monte-Carlo method assisted by a Gaussian-processes regression model. These observations were taken as part of the University of Wyoming's 2017 Research Experience for Undergraduates (REU) and represent one of multiple hot Jupiter exoplanet targets for which we have transit event observations in multiple broadband filters.
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USDA-ARS?s Scientific Manuscript database
Understanding your goals in life will assist you identifying the right career path. As we transition from an undergraduate student into our professional career there are an array of skills we will require over the years. This leads to, how do we stand out from the crowd? Here I discuss how I transit...
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Energy management during the space shuttle transition
NASA Technical Reports Server (NTRS)
Stengel, R. F.
1972-01-01
An approach to calculating optimal, gliding flight paths of the type associated with the space shuttle's transition from entry to cruising flight is presented. Kinetic energy and total energy (per unit weight) replace velocity and time in the dynamic equations, reducing the dimension and complexity of the problem. The capability for treating integral and terminal penalties (as well as Mach number effects) is retained in the numerical optimization; hence, stability and control boundaries can be observed as trajectories to the desired final energy, flight path angle, and range are determined. Numerical results show that the jump to the front-side of the L/D curve need not be made until the end of the transition and that the dynamic model provides a conservative range estimate. Alternatives for real time trajectory control are discussed.
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Unzip instabilities: Straight to oscillatory transitions in the cutting of thin polymer sheets
NASA Astrophysics Data System (ADS)
Reis, P. M.; Kumar, A.; Shattuck, M. D.; Roman, B.
2008-06-01
We report an experimental investigation of the cutting of a thin brittle polymer sheet with a blunt tool. It was recently shown that the fracture path becomes oscillatory when the tool is much wider than the sheet thickness. Here we uncover two novel transitions from straight to oscillatory fracture by varying either the tilt angle of the tool or the speed of cutting, respectively. We denote these by angle and speed unzip instabilities and analyze them by quantifying both the dynamics of the crack tip and the final shapes of the fracture paths. Moreover, for the speed unzip instability, the straight crack lip obtained at low speeds exhibits out-of-plane buckling undulations (as opposed to being flat above the instability threshold) suggesting a transition from ductile to brittle fracture.
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Low carbon transition and sustainable development path of tourism industry
NASA Astrophysics Data System (ADS)
Zhu, Hongbing; Zhang, Jing; Zhao, Lei; Jin, Shenglang
2017-05-01
The low carbon transition is as much a transformative technology shift as it represents a response to global environment challenges. The low carbon paradigm presents a new direction of change for tourism industry. However, the lack of theoretical frameworks on low carbon transformation in tourism industry context provides a significant knowledge gap. This paper firstly investigates the relationships between low carbon and sustainable development, followed by exploring the existing challenges of tourism sustainable development. At last, this paper presents a sustainable development path framework for low carbon transition of tourism industry, which include accelerating deployment of renewable energy, energy-saving green building construction, improving green growth investment, and adopting a sustainable consumption and production system, in order to promote energy and water efficiency, waste management, GHG emissions mitigation and eventually enhance its sustainability.
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A one-way shooting algorithm for transition path sampling of asymmetric barriers
NASA Astrophysics Data System (ADS)
Brotzakis, Z. Faidon; Bolhuis, Peter G.
2016-10-01
We present a novel transition path sampling shooting algorithm for the efficient sampling of complex (biomolecular) activated processes with asymmetric free energy barriers. The method employs a fictitious potential that biases the shooting point toward the transition state. The method is similar in spirit to the aimless shooting technique by Peters and Trout [J. Chem. Phys. 125, 054108 (2006)], but is targeted for use with the one-way shooting approach, which has been shown to be more effective than two-way shooting algorithms in systems dominated by diffusive dynamics. We illustrate the method on a 2D Langevin toy model, the association of two peptides and the initial step in dissociation of a β-lactoglobulin dimer. In all cases we show a significant increase in efficiency.
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Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; ...
2017-03-08
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structuremore » of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.« less
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NASA Astrophysics Data System (ADS)
Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; Kathuria, Sagar V.; Bilsel, Osman; Matthews, C. Robert; Lane, T. J.; Pande, Vijay S.
2017-03-01
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.
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Resonant optical spectroscopy and coherent control of C r4 + spin ensembles in SiC and GaN
NASA Astrophysics Data System (ADS)
Koehl, William F.; Diler, Berk; Whiteley, Samuel J.; Bourassa, Alexandre; Son, N. T.; Janzén, Erik; Awschalom, David D.
2017-01-01
Spins bound to point defects are increasingly viewed as an important resource for solid-state implementations of quantum information and spintronic technologies. In particular, there is a growing interest in the identification of new classes of defect spin that can be controlled optically. Here, we demonstrate ensemble optical spin polarization and optically detected magnetic resonance (ODMR) of the S = 1 electronic ground state of chromium (C r4 + ) impurities in silicon carbide (SiC) and gallium nitride (GaN). Spin polarization is made possible by the narrow optical linewidths of these ensembles (<8.5 GHz), which are similar in magnitude to the ground state zero-field spin splitting energies of the ions at liquid helium temperatures. This allows us to optically resolve individual spin sublevels within the ensembles at low magnetic fields using resonant excitation from a cavity-stabilized, narrow-linewidth laser. Additionally, these near-infrared emitters possess exceptionally weak phonon sidebands, ensuring that >73% of the overall optical emission is contained with the defects' zero-phonon lines. These characteristics make this semiconductor-based, transition metal impurity system a promising target for further study in the ongoing effort to integrate optically active quantum states within common optoelectronic materials.
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Folguera-Blasco, Núria; Cuyàs, Elisabet; Menéndez, Javier A; Alarcón, Tomás
2018-03-01
Understanding the control of epigenetic regulation is key to explain and modify the aging process. Because histone-modifying enzymes are sensitive to shifts in availability of cofactors (e.g. metabolites), cellular epigenetic states may be tied to changing conditions associated with cofactor variability. The aim of this study is to analyse the relationships between cofactor fluctuations, epigenetic landscapes, and cell state transitions. Using Approximate Bayesian Computation, we generate an ensemble of epigenetic regulation (ER) systems whose heterogeneity reflects variability in cofactor pools used by histone modifiers. The heterogeneity of epigenetic metabolites, which operates as regulator of the kinetic parameters promoting/preventing histone modifications, stochastically drives phenotypic variability. The ensemble of ER configurations reveals the occurrence of distinct epi-states within the ensemble. Whereas resilient states maintain large epigenetic barriers refractory to reprogramming cellular identity, plastic states lower these barriers, and increase the sensitivity to reprogramming. Moreover, fine-tuning of cofactor levels redirects plastic epigenetic states to re-enter epigenetic resilience, and vice versa. Our ensemble model agrees with a model of metabolism-responsive loss of epigenetic resilience as a cellular aging mechanism. Our findings support the notion that cellular aging, and its reversal, might result from stochastic translation of metabolic inputs into resilient/plastic cell states via ER systems.
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Resonant optical spectroscopy and coherent control of C r 4 + spin ensembles in SiC and GaN
Koehl, William F.; Diler, Berk; Whiteley, Samuel J.; ...
2017-01-15
Spins bound to point defects are increasingly viewed as an important resource for solid-state implementations of quantum information technologies. In particular, there is a growing interest in the identification of new classes of defect spin that can be controlled optically. Here we demonstrate ensemble optical spin polarization and optically detected magnetic resonance (ODMR) of the S = 1 electronic ground state of chromium (Cr 4+) impurities in silicon carbide (SiC) and gallium nitride (GaN). Polarization is made possible by the narrow optical linewidths of these ensembles (< 8.5 GHz), which are similar in magnitude to the ground state zero-field spinmore » splitting energies of the ions at liquid helium temperatures. We therefore are able to optically resolve individual spin sublevels within the ensembles at low magnetic fields using resonant excitation from a cavity-stabilized, narrow-linewidth laser. Additionally, these near-infrared emitters possess exceptionally weak phonon sidebands, ensuring that > 73% of the overall optical emission is contained with the defects’ zero-phonon lines. Lastly, these characteristics make this semiconductor-based, transition metal impurity system a promising target for further study in the ongoing effort to integrate optically active quantum states within common optoelectronic materials.« less
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Development of FB-MultiPier dynamic vessel-collision analysis models, phase 2.
DOT National Transportation Integrated Search
2014-07-01
Massive waterway vessels such as barges regularly transit navigable waterways in the U.S. During passages that fall within : the vicinity of bridge structures, vessels may (under extreme circumstances) deviate from the intended vessel transit path. A...
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West, Michael D.; Labat, Ivan; Sternberg, Hal; Larocca, Dana; Nasonkin, Igor; Chapman, Karen B.; Singh, Ratnesh; Makarev, Eugene; Aliper, Alex; Kazennov, Andrey; Alekseenko, Andrey; Shuvalov, Nikolai; Cheskidova, Evgenia; Alekseev, Aleksandr; Artemov, Artem; Putin, Evgeny; Mamoshina, Polina; Pryanichnikov, Nikita; Larocca, Jacob; Copeland, Karen; Izumchenko, Evgeny; Korzinkin, Mikhail; Zhavoronkov, Alex
2018-01-01
Here we present the application of deep neural network (DNN) ensembles trained on transcriptomic data to identify the novel markers associated with the mammalian embryonic-fetal transition (EFT). Molecular markers of this process could provide important insights into regulatory mechanisms of normal development, epimorphic tissue regeneration and cancer. Subsequent analysis of the most significant genes behind the DNNs classifier on an independent dataset of adult-derived and human embryonic stem cell (hESC)-derived progenitor cell lines led to the identification of COX7A1 gene as a potential EFT marker. COX7A1, encoding a cytochrome C oxidase subunit, was up-regulated in post-EFT murine and human cells including adult stem cells, but was not expressed in pre-EFT pluripotent embryonic stem cells or their in vitro-derived progeny. COX7A1 expression level was observed to be undetectable or low in multiple sarcoma and carcinoma cell lines as compared to normal controls. The knockout of the gene in mice led to a marked glycolytic shift reminiscent of the Warburg effect that occurs in cancer cells. The DNN approach facilitated the elucidation of a potentially new biomarker of cancer and pre-EFT cells, the embryo-onco phenotype, which may potentially be used as a target for controlling the embryonic-fetal transition. PMID:29487692
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West, Michael D; Labat, Ivan; Sternberg, Hal; Larocca, Dana; Nasonkin, Igor; Chapman, Karen B; Singh, Ratnesh; Makarev, Eugene; Aliper, Alex; Kazennov, Andrey; Alekseenko, Andrey; Shuvalov, Nikolai; Cheskidova, Evgenia; Alekseev, Aleksandr; Artemov, Artem; Putin, Evgeny; Mamoshina, Polina; Pryanichnikov, Nikita; Larocca, Jacob; Copeland, Karen; Izumchenko, Evgeny; Korzinkin, Mikhail; Zhavoronkov, Alex
2018-01-30
Here we present the application of deep neural network (DNN) ensembles trained on transcriptomic data to identify the novel markers associated with the mammalian embryonic-fetal transition (EFT). Molecular markers of this process could provide important insights into regulatory mechanisms of normal development, epimorphic tissue regeneration and cancer. Subsequent analysis of the most significant genes behind the DNNs classifier on an independent dataset of adult-derived and human embryonic stem cell (hESC)-derived progenitor cell lines led to the identification of COX7A1 gene as a potential EFT marker. COX7A1 , encoding a cytochrome C oxidase subunit, was up-regulated in post-EFT murine and human cells including adult stem cells, but was not expressed in pre-EFT pluripotent embryonic stem cells or their in vitro -derived progeny. COX7A1 expression level was observed to be undetectable or low in multiple sarcoma and carcinoma cell lines as compared to normal controls. The knockout of the gene in mice led to a marked glycolytic shift reminiscent of the Warburg effect that occurs in cancer cells. The DNN approach facilitated the elucidation of a potentially new biomarker of cancer and pre-EFT cells, the embryo-onco phenotype, which may potentially be used as a target for controlling the embryonic-fetal transition.
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Blum, Christian; Meixner, Alfred J; Subramaniam, Vinod
2004-12-01
It is known from ensemble spectroscopy at cryogenic temperatures that variants of the Aequorea green fluorescent protein (GFP) occur in interconvertible spectroscopically distinct forms which are obscured in ensemble room temperature spectroscopy. By analyzing the fluorescence of the GFP variants EYFP and EGFP by spectrally resolved single-molecule spectroscopy we were able to observe spectroscopically different forms of the proteins and to dynamically monitor transitions between these forms at room temperature. In addition to the predominant EYFP B-form we have observed the blue-shifted I-form thus far only seen at cryogenic temperatures and have followed transitions between these forms. Further we have identified for EYFP and for EGFP three more, so far unknown, forms with red-shifted fluorescence. Transitions between the predominant forms and the red-shifted forms show a dark time which indicates the existence of a nonfluorescent intermediate. The spectral position of the newly-identified red-shifted forms and their formation via a nonfluorescent intermediate hint that these states may account for the possible photoactivation observed in bulk experiments. The comparison of the single-protein spectra of the red-shifted EYFP and EGFP forms with single-molecule fluorescence spectra of DsRed suggest that these new forms possibly originate from an extended chromophoric pi-system analogous to the DsRed chromophore.
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Superfluid-insulator transitions of two-species bosons in an optical lattice
DOE Office of Scientific and Technical Information (OSTI.GOV)
Isacsson, A.; Department of Physics, Yale University, P.O. Box 208120, New Haven, Connecticut 06520-8120; Cha, M.-C.
2005-11-01
We consider the two-species bosonic Hubbard model with variable interspecies interaction and hopping strength in the grand canonical ensemble with a common chemical potential. We analyze the superfluid-insulator (SI) transition for the relevant parameter regimes and compute the ground state phase diagram in the vicinity of odd filling Mott states. We find that the superfluid-insulator transition occurs with (a) simultaneous onset of superfluidity of both species or (b) coexistence of Mott insulating state of one species and superfluidity of the other or, in the case of unit filling (c) complete depopulation of one species. The superfluid-insulator transition can be firstmore » order in a large region of the phase diagram. We develop a variational mean-field method which takes into account the effect of second order quantum fluctuations on the superfluid-insulator transition and corroborate the mean-field phase diagram using a quantum Monte Carlo study.« less
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Statistical thermodynamics of clustered populations.
Matsoukas, Themis
2014-08-01
We present a thermodynamic theory for a generic population of M individuals distributed into N groups (clusters). We construct the ensemble of all distributions with fixed M and N, introduce a selection functional that embodies the physics that governs the population, and obtain the distribution that emerges in the scaling limit as the most probable among all distributions consistent with the given physics. We develop the thermodynamics of the ensemble and establish a rigorous mapping to regular thermodynamics. We treat the emergence of a so-called giant component as a formal phase transition and show that the criteria for its emergence are entirely analogous to the equilibrium conditions in molecular systems. We demonstrate the theory by an analytic model and confirm the predictions by Monte Carlo simulation.
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NASA Astrophysics Data System (ADS)
Kota, V. K. B.
2003-07-01
Smoothed forms for expectation values < K> E of positive definite operators K follow from the K-density moments either directly or in many other ways each giving a series expansion (involving polynomials in E). In large spectroscopic spaces one has to partition the many particle spaces into subspaces. Partitioning leads to new expansions for expectation values. It is shown that all the expansions converge to compact forms depending on the nature of the operator K and the operation of embedded random matrix ensembles and quantum chaos in many particle spaces. Explicit results are given for occupancies < ni> E, spin-cutoff factors < JZ2> E and strength sums < O†O> E, where O is a one-body transition operator.
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Exactly solvable random graph ensemble with extensively many short cycles
NASA Astrophysics Data System (ADS)
Aguirre López, Fabián; Barucca, Paolo; Fekom, Mathilde; Coolen, Anthony C. C.
2018-02-01
We introduce and analyse ensembles of 2-regular random graphs with a tuneable distribution of short cycles. The phenomenology of these graphs depends critically on the scaling of the ensembles’ control parameters relative to the number of nodes. A phase diagram is presented, showing a second order phase transition from a connected to a disconnected phase. We study both the canonical formulation, where the size is large but fixed, and the grand canonical formulation, where the size is sampled from a discrete distribution, and show their equivalence in the thermodynamical limit. We also compute analytically the spectral density, which consists of a discrete set of isolated eigenvalues, representing short cycles, and a continuous part, representing cycles of diverging size.
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NASA Astrophysics Data System (ADS)
Li, Liang-Sheng
2016-12-01
We explore the tricritical points and the critical lines of both Blume-Emery-Grifnths and Ising model within long-range interactions in the microcanonical ensemble. For K = K MTP , the tricritical exponents take the values β = 1/4, 1 = γ- ≠ γ+ = 1/2 and 0 = α- ≠ α+ = -1/2, which disagree with classical (mean held) values. When K > K MTP , the phase transition becomes second order and the critical exponents have classical values except close to the canonical tricritical parameters (K CTP ), where the values of the critical expoents become β = 1/2, 1 = γ- ≠ γ+ = 2 and 0 = α- ≠ α+ = 1. Supported by the National Natural Science Foundation of China under Grant No. 11104032
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Verification of Ensemble Forecasts for the New York City Operations Support Tool
NASA Astrophysics Data System (ADS)
Day, G.; Schaake, J. C.; Thiemann, M.; Draijer, S.; Wang, L.
2012-12-01
The New York City water supply system operated by the Department of Environmental Protection (DEP) serves nine million people. It covers 2,000 square miles of portions of the Catskill, Delaware, and Croton watersheds, and it includes nineteen reservoirs and three controlled lakes. DEP is developing an Operations Support Tool (OST) to support its water supply operations and planning activities. OST includes historical and real-time data, a model of the water supply system complete with operating rules, and lake water quality models developed to evaluate alternatives for managing turbidity in the New York City Catskill reservoirs. OST will enable DEP to manage turbidity in its unfiltered system while satisfying its primary objective of meeting the City's water supply needs, in addition to considering secondary objectives of maintaining ecological flows, supporting fishery and recreation releases, and mitigating downstream flood peaks. The current version of OST relies on statistical forecasts of flows in the system based on recent observed flows. To improve short-term decision making, plans are being made to transition to National Weather Service (NWS) ensemble forecasts based on hydrologic models that account for short-term weather forecast skill, longer-term climate information, as well as the hydrologic state of the watersheds and recent observed flows. To ensure that the ensemble forecasts are unbiased and that the ensemble spread reflects the actual uncertainty of the forecasts, a statistical model has been developed to post-process the NWS ensemble forecasts to account for hydrologic model error as well as any inherent bias and uncertainty in initial model states, meteorological data and forecasts. The post-processor is designed to produce adjusted ensemble forecasts that are consistent with the DEP historical flow sequences that were used to develop the system operating rules. A set of historical hindcasts that is representative of the real-time ensemble forecasts is needed to verify that the post-processed forecasts are unbiased, statistically reliable, and preserve the skill inherent in the "raw" NWS ensemble forecasts. A verification procedure and set of metrics will be presented that provide an objective assessment of ensemble forecasts. The procedure will be applied to both raw ensemble hindcasts and to post-processed ensemble hindcasts. The verification metrics will be used to validate proper functioning of the post-processor and to provide a benchmark for comparison of different types of forecasts. For example, current NWS ensemble forecasts are based on climatology, using each historical year to generate a forecast trace. The NWS Hydrologic Ensemble Forecast System (HEFS) under development will utilize output from both the National Oceanic Atmospheric Administration (NOAA) Global Ensemble Forecast System (GEFS) and the Climate Forecast System (CFS). Incorporating short-term meteorological forecasts and longer-term climate forecast information should provide sharper, more accurate forecasts. Hindcasts from HEFS will enable New York City to generate verification results to validate the new forecasts and further fine-tune system operating rules. Project verification results will be presented for different watersheds across a range of seasons, lead times, and flow levels to assess the quality of the current ensemble forecasts.
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Stochastic Cell Fate Progression in Embryonic Stem Cells
NASA Astrophysics Data System (ADS)
Zou, Ling-Nan; Doyle, Adele; Jang, Sumin; Ramanathan, Sharad
2013-03-01
Studies on the directed differentiation of embryonic stem (ES) cells suggest that some early developmental decisions may be stochastic in nature. To identify the sources of this stochasticity, we analyzed the heterogeneous expression of key transcription factors in single ES cells as they adopt distinct germ layer fates. We find that under sufficiently stringent signaling conditions, the choice of lineage is unambiguous. ES cells flow into differentiated fates via diverging paths, defined by sequences of transitional states that exhibit characteristic co-expression of multiple transcription factors. These transitional states have distinct responses to morphogenic stimuli; by sequential exposure to multiple signaling conditions, ES cells are steered towards specific fates. However, the rate at which cells travel down a developmental path is stochastic: cells exposed to the same signaling condition for the same amount of time can populate different states along the same path. The heterogeneity of cell states seen in our experiments therefore does not reflect the stochastic selection of germ layer fates, but the stochastic rate of progression along a chosen developmental path. Supported in part by the Jane Coffin Childs Fund
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Total probabilities of ensemble runoff forecasts
NASA Astrophysics Data System (ADS)
Olav Skøien, Jon; Bogner, Konrad; Salamon, Peter; Smith, Paul; Pappenberger, Florian
2016-04-01
Ensemble forecasting has for a long time been used as a method in meteorological modelling to indicate the uncertainty of the forecasts. However, as the ensembles often exhibit both bias and dispersion errors, it is necessary to calibrate and post-process them. Two of the most common methods for this are Bayesian Model Averaging (Raftery et al., 2005) and Ensemble Model Output Statistics (EMOS) (Gneiting et al., 2005). There are also methods for regionalizing these methods (Berrocal et al., 2007) and for incorporating the correlation between lead times (Hemri et al., 2013). Engeland and Steinsland Engeland and Steinsland (2014) developed a framework which can estimate post-processing parameters which are different in space and time, but still can give a spatially and temporally consistent output. However, their method is computationally complex for our larger number of stations, and cannot directly be regionalized in the way we would like, so we suggest a different path below. The target of our work is to create a mean forecast with uncertainty bounds for a large number of locations in the framework of the European Flood Awareness System (EFAS - http://www.efas.eu) We are therefore more interested in improving the forecast skill for high-flows rather than the forecast skill of lower runoff levels. EFAS uses a combination of ensemble forecasts and deterministic forecasts from different forecasters to force a distributed hydrologic model and to compute runoff ensembles for each river pixel within the model domain. Instead of showing the mean and the variability of each forecast ensemble individually, we will now post-process all model outputs to find a total probability, the post-processed mean and uncertainty of all ensembles. The post-processing parameters are first calibrated for each calibration location, but assuring that they have some spatial correlation, by adding a spatial penalty in the calibration process. This can in some cases have a slight negative impact on the calibration error, but makes it easier to interpolate the post-processing parameters to uncalibrated locations. We also look into different methods for handling the non-normal distributions of runoff data and the effect of different data transformations on forecasts skills in general and for floods in particular. Berrocal, V. J., Raftery, A. E. and Gneiting, T.: Combining Spatial Statistical and Ensemble Information in Probabilistic Weather Forecasts, Mon. Weather Rev., 135(4), 1386-1402, doi:10.1175/MWR3341.1, 2007. Engeland, K. and Steinsland, I.: Probabilistic postprocessing models for flow forecasts for a system of catchments and several lead times, Water Resour. Res., 50(1), 182-197, doi:10.1002/2012WR012757, 2014. Gneiting, T., Raftery, A. E., Westveld, A. H. and Goldman, T.: Calibrated Probabilistic Forecasting Using Ensemble Model Output Statistics and Minimum CRPS Estimation, Mon. Weather Rev., 133(5), 1098-1118, doi:10.1175/MWR2904.1, 2005. Hemri, S., Fundel, F. and Zappa, M.: Simultaneous calibration of ensemble river flow predictions over an entire range of lead times, Water Resour. Res., 49(10), 6744-6755, doi:10.1002/wrcr.20542, 2013. Raftery, A. E., Gneiting, T., Balabdaoui, F. and Polakowski, M.: Using Bayesian Model Averaging to Calibrate Forecast Ensembles, Mon. Weather Rev., 133(5), 1155-1174, doi:10.1175/MWR2906.1, 2005.
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NASA Astrophysics Data System (ADS)
Iachimciuc, Igor
The dissertation is in two parts, a theoretical study and a musical composition. In Part I the music of Gyorgy Kurtag is analyzed from the point of view of sound color. A brief description of what is understood by the term sound color, and various ways of achieving specific coloristic effects, are presented in the Introduction. An examination of Kurtag's approaches to the domain of sound color occupies the chapters that follow. The musical examples that are analyzed are selected from Kurtag's different compositional periods, showing a certain consistency in sound color techniques, the most important of which are already present in the String Quartet, Op. 1. The compositions selected for analysis are written for different ensembles, but regardless of the instrumentation, certain principles of the formation and organization of sound color remain the same. Rather than relying on extended instrumental techniques, Kurtag creates a large variety of sound colors using traditional means such as pitch material, register, density, rhythm, timbral combinations, dynamics, texture, spatial displacement of the instruments, and the overall musical context. Each sound color unit in Kurtag's music is a separate entity, conceived as a complete microcosm. Sound color units can either be juxtaposed as contrasting elements, forming sound color variations, or superimposed, often resulting in a Klangfarbenmelodie effect. Some of the same gestural figures (objets trouves) appear in different compositions, but with significant coloristic modifications. Thus, the principle of sound color variations is not only a strong organizational tool, but also a characteristic stylistic feature of the music of Gyorgy Kurtag. Part II, Leopard's Path (2010), for flute, clarinet, violin, cello, cimbalom, and piano, is an original composition inspired by the painting of Jesse Allen, a San Francisco based artist. The composition is conceived as a cycle of thirteen short movements. Ten of these movements are the musical interpretation of the objects presented in the painting, and are stylistically similar. These movements are scored for the entire ensemble. The other three movements, entitled Interludes, provide a stylistic contrast, and are not directly connected with the painting.
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NASA Astrophysics Data System (ADS)
Lee, Sang-Min; Nam, Ji-Eun; Choi, Hee-Wook; Ha, Jong-Chul; Lee, Yong Hee; Kim, Yeon-Hee; Kang, Hyun-Suk; Cho, ChunHo
2016-08-01
This study was conducted to evaluate the prediction accuracies of THe Observing system Research and Predictability EXperiment (THORPEX) Interactive Grand Global Ensemble (TIGGE) data at six operational forecast centers using the root-mean square difference (RMSD) and Brier score (BS) from April to July 2012. And it was performed to test the precipitation predictability of ensemble prediction systems (EPS) on the onset of the summer rainy season, the day of withdrawal in spring drought over South Korea on 29 June 2012 with use of the ensemble mean precipitation, ensemble probability precipitation, 10-day lag ensemble forecasts (ensemble mean and probability precipitation), and effective drought index (EDI). The RMSD analysis of atmospheric variables (geopotential-height at 500 hPa, temperature at 850 hPa, sea-level pressure and specific humidity at 850 hPa) showed that the prediction accuracies of the EPS at the Meteorological Service of Canada (CMC) and China Meteorological Administration (CMA) were poor and those at the European Center for Medium-Range Weather Forecasts (ECMWF) and Korea Meteorological Administration (KMA) were good. Also, ECMWF and KMA showed better results than other EPSs for predicting precipitation in the BS distributions. It is also evaluated that the onset of the summer rainy season could be predicted using ensemble-mean precipitation from 4-day leading time at all forecast centers. In addition, the spatial distributions of predicted precipitation of the EPS at KMA and the Met Office of the United Kingdom (UKMO) were similar to those of observed precipitation; thus, the predictability showed good performance. The precipitation probability forecasts of EPS at CMA, the National Centers for Environmental Prediction (NCEP), and UKMO (ECMWF and KMA) at 1-day lead time produced over-forecasting (under-forecasting) in the reliability diagram. And all the ones at 2˜4-day lead time showed under-forecasting. Also, the precipitation on onset day of the summer rainy season could be predicted from a 4-day lead time to initial time by using the 10-day lag ensemble mean and probability forecasts. Additionally, the predictability for withdrawal day of spring drought to be ended due to precipitation on onset day of summer rainy season was evaluated using Effective Drought Index (EDI) to be calculated by ensemble mean precipitation forecasts and spreads at five EPSs.
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NASA Astrophysics Data System (ADS)
Forrester, Peter J.; Trinh, Allan K.
2018-05-01
The neighbourhood of the largest eigenvalue λmax in the Gaussian unitary ensemble (GUE) and Laguerre unitary ensemble (LUE) is referred to as the soft edge. It is known that there exists a particular centring and scaling such that the distribution of λmax tends to a universal form, with an error term bounded by 1/N2/3. We take up the problem of computing the exact functional form of the leading error term in a large N asymptotic expansion for both the GUE and LUE—two versions of the LUE are considered, one with the parameter a fixed and the other with a proportional to N. Both settings in the LUE case allow for an interpretation in terms of the distribution of a particular weighted path length in a model involving exponential variables on a rectangular grid, as the grid size gets large. We give operator theoretic forms of the corrections, which are corollaries of knowledge of the first two terms in the large N expansion of the scaled kernel and are readily computed using a method due to Bornemann. We also give expressions in terms of the solutions of particular systems of coupled differential equations, which provide an alternative method of computation. Both characterisations are well suited to a thinned generalisation of the original ensemble, whereby each eigenvalue is deleted independently with probability (1 - ξ). In Sec. V, we investigate using simulation the question of whether upon an appropriate centring and scaling a wider class of complex Hermitian random matrix ensembles have their leading correction to the distribution of λmax proportional to 1/N2/3.
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Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods.
Notaro, Marco; Schubach, Max; Robinson, Peter N; Valentini, Giorgio
2017-10-12
The prediction of human gene-abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with a specific disease. In this context the Human Phenotype Ontology (HPO) provides a standard categorization of the abnormalities associated with human diseases. While the problem of the prediction of gene-disease associations has been widely investigated, the related problem of gene-phenotypic feature (i.e., HPO term) associations has been largely overlooked, even if for most human genes no HPO term associations are known and despite the increasing application of the HPO to relevant medical problems. Moreover most of the methods proposed in literature are not able to capture the hierarchical relationships between HPO terms, thus resulting in inconsistent and relatively inaccurate predictions. We present two hierarchical ensemble methods that we formally prove to provide biologically consistent predictions according to the hierarchical structure of the HPO. The modular structure of the proposed methods, that consists in a "flat" learning first step and a hierarchical combination of the predictions in the second step, allows the predictions of virtually any flat learning method to be enhanced. The experimental results show that hierarchical ensemble methods are able to predict novel associations between genes and abnormal phenotypes with results that are competitive with state-of-the-art algorithms and with a significant reduction of the computational complexity. Hierarchical ensembles are efficient computational methods that guarantee biologically meaningful predictions that obey the true path rule, and can be used as a tool to improve and make consistent the HPO terms predictions starting from virtually any flat learning method. The implementation of the proposed methods is available as an R package from the CRAN repository.
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NASA Astrophysics Data System (ADS)
Yettella, Vineel; Kay, Jennifer E.
2017-09-01
The extratropical precipitation response to global warming is investigated within a 30-member initial condition climate model ensemble. As in observations, modeled cyclonic precipitation contributes a large fraction of extratropical precipitation, especially over the ocean and in the winter hemisphere. When compared to present day, the ensemble projects increased cyclone-associated precipitation under twenty-first century business-as-usual greenhouse gas forcing. While the cyclone-associated precipitation response is weaker in the near-future (2016-2035) than in the far-future (2081-2100), both future periods have similar patterns of response. Though cyclone frequency changes are important regionally, most of the increased cyclone-associated precipitation results from increased within-cyclone precipitation. Consistent with this result, cyclone-centric composites show statistically significant precipitation increases in all cyclone sectors. Decomposition into thermodynamic (mean cyclone water vapor path) and dynamic (mean cyclone wind speed) contributions shows that thermodynamics explains 92 and 95% of the near-future and far-future within-cyclone precipitation increases respectively. Surprisingly, the influence of dynamics on future cyclonic precipitation changes is negligible. In addition, the forced response exceeds internal variability in both future time periods. Overall, this work suggests that future cyclonic precipitation changes will result primarily from increased moisture availability in a warmer world, with secondary contributions from changes in cyclone frequency and cyclone dynamics.
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Transition Specialists Partner with Students to Turn Dreams into Reality
ERIC Educational Resources Information Center
Flannery, Ann
2013-01-01
Ann Flannery is one of two transition specialists who serve youth and families statewide through the Post-Secondary Transition Program of the Idaho Educational Services for the Deaf and the Blind. In this article she writes that too often her office was seeing graduates coming back to school after failing to find a path to success. They returned…
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ERIC Educational Resources Information Center
Tchalakov, Ivan; Mitev, Tihomir; Petrov, Venelin
2010-01-01
The paper questions some of the premises in studying academic spin-offs in developed countries, claiming that when taken as characteristics of "academic spin-offs per se," they are of little help in understanding the phenomenon in the Eastern European countries during the transitional and post-transitional periods after 1989. It argues…
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ERIC Educational Resources Information Center
Lyons, Guy Kevin
2014-01-01
Students face many challenges in the transition to high school. From pressures of high-stakes testing for graduation to transitioning to the high school environment, many diversions can delay or even stop a student's path to graduation. Ninth-grade students are at a pivotal point in their educational careers, and a successful transition to high…
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Energy barrier of bcc-fcc phase transition via the Bain path in Yukawa system
NASA Astrophysics Data System (ADS)
Kiyokawa, Shuji
2018-05-01
In the Yukawa system with the dimensionless screening parameter κ>1.5 , when bcc-fcc transition occurs via Bain path, we show that spontaneous transitions do not occur even if the system temperature reaches the transition point of bcc-fcc because it is necessary to increase once the free energy in the process of transition from bcc to fcc through Bain deformation. Here, we refer the temporary increment of the free energy during Bain deformation as Bain barrier. Since there are the Bain barriers at the transitions between bcc and fcc phases, these phases may coexist as metastable state in the wide region (not a coexistence line) of κ and the coupling constant Γ. We study the excess energy of the system and the free energy difference between bcc and fcc phases by the Monte Carlo method, where the simulation box is divided into a large number of elements with small volume and a particle in the box is restricted be placed in one of these elements. By this method, we can tabulate the values of the interparticle potential and can calculate the internal energy fast and precisely.
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Wille, M-L; Zapf, M; Ruiter, N V; Gemmeke, H; Langton, C M
2015-06-21
The quality of ultrasound computed tomography imaging is primarily determined by the accuracy of ultrasound transit time measurement. A major problem in analysis is the overlap of signals making it difficult to detect the correct transit time. The current standard is to apply a matched-filtering approach to the input and output signals. This study compares the matched-filtering technique with active set deconvolution to derive a transit time spectrum from a coded excitation chirp signal and the measured output signal. The ultrasound wave travels in a direct and a reflected path to the receiver, resulting in an overlap in the recorded output signal. The matched-filtering and deconvolution techniques were applied to determine the transit times associated with the two signal paths. Both techniques were able to detect the two different transit times; while matched-filtering has a better accuracy (0.13 μs versus 0.18 μs standard deviations), deconvolution has a 3.5 times improved side-lobe to main-lobe ratio. A higher side-lobe suppression is important to further improve image fidelity. These results suggest that a future combination of both techniques would provide improved signal detection and hence improved image fidelity.
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Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein
Day, Ryan; Paschek, Dietmar; Garcia, Angel E.
2012-01-01
We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169
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Different realizations of Cooper-Frye sampling with conservation laws
NASA Astrophysics Data System (ADS)
Schwarz, C.; Oliinychenko, D.; Pang, L.-G.; Ryu, S.; Petersen, H.
2018-01-01
Approaches based on viscous hydrodynamics for the hot and dense stage and hadronic transport for the final dilute rescattering stage are successfully applied to the dynamic description of heavy ion reactions at high beam energies. One crucial step in such hybrid approaches is the so-called particlization, which is the transition between the hydrodynamic description and the microscopic degrees of freedom. For this purpose, individual particles are sampled on the Cooper-Frye hypersurface. In this work, four different realizations of the sampling algorithms are compared, with three of them incorporating the global conservation laws of quantum numbers in each event. The algorithms are compared within two types of scenarios: a simple ‘box’ hypersurface consisting of only one static cell and a typical particlization hypersurface for Au+Au collisions at \\sqrt{{s}{NN}}=200 {GeV}. For all algorithms the mean multiplicities (or particle spectra) remain unaffected by global conservation laws in the case of large volumes. In contrast, the fluctuations of the particle numbers are affected considerably. The fluctuations of the newly developed SPREW algorithm based on the exponential weight, and the recently suggested SER algorithm based on ensemble rejection, are smaller than those without conservation laws and agree with the expectation from the canonical ensemble. The previously applied mode sampling algorithm produces dramatically larger fluctuations than expected in the corresponding microcanonical ensemble, and therefore should be avoided in fluctuation studies. This study might be of interest for the investigation of particle fluctuations and correlations, e.g. the suggested signatures for a phase transition or a critical endpoint, in hybrid approaches that are affected by global conservation laws.
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NASA Astrophysics Data System (ADS)
Yang, Bo; Li, Xiao-Teng; Chen, Wei; Liu, Jian; Chen, Xiao-Song
2016-10-01
Self-questioning mechanism which is similar to single spin-flip of Ising model in statistical physics is introduced into spatial evolutionary game model. We propose a game model with altruistic to spiteful preferences via weighted sums of own and opponent's payoffs. This game model can be transformed into Ising model with an external field. Both interaction between spins and the external field are determined by the elements of payoff matrix and the preference parameter. In the case of perfect rationality at zero social temperature, this game model has three different phases which are entirely cooperative phase, entirely non-cooperative phase and mixed phase. In the investigations of the game model with Monte Carlo simulation, two paths of payoff and preference parameters are taken. In one path, the system undergoes a discontinuous transition from cooperative phase to non-cooperative phase with the change of preference parameter. In another path, two continuous transitions appear one after another when system changes from cooperative phase to non-cooperative phase with the prefenrence parameter. The critical exponents v, β, and γ of two continuous phase transitions are estimated by the finite-size scaling analysis. Both continuous phase transitions have the same critical exponents and they belong to the same universality class as the two-dimensional Ising model. Supported by the National Natural Science Foundation of China under Grant Nos. 11121403 and 11504384
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NASA Astrophysics Data System (ADS)
Pasquier, Benoît; Holzer, Mark
2016-08-01
We systematically quantify the pathways and time scales that set the efficiency, Ebio, of the global biological pump by applying Green-function-based diagnostics to a data-assimilated phosphorus cycle embedded in a jointly assimilated ocean circulation. We consider "bio pipes" that consist of phosphorus paths that connect specified regions of last biological utilization with regions where regenerated phosphate first reemerges into the euphotic zone. The bio pipes that contribute most to Ebio connect the Eastern Equatorial Pacific (EEqP) and Equatorial Atlantic to the Southern Ocean ((21 ± 3)% of Ebio), as well as the Southern Ocean to itself ((15 ± 3)% of Ebio). The bio pipes with the largest phosphorus flow rates connect the EEqP to itself and the subantarctic Southern Ocean to itself. The global mean sequestration time of the biological pump is 130 ± 70 years, while the sequestration time of the bio pipe from anywhere to the Antarctic region of the Southern Ocean is 430 ± 30 years. The distribution of phosphorus flowing within a given bio pipe is quantified by its transit-time partitioned path density. For the largest bio pipes, ˜1/7 of their phosphorus is carried by thermocline paths with transit times less than ˜300-400 years, while ˜4/7 of their phosphorus is carried by abyssal paths with transit times exceeding ˜700 years. The path density reveals that Antarctic Intermediate Water carries about a third of the regenerated phosphate last utilized in the EEqP that is destined for the Southern Ocean euphotic zone. The Southern Ocean is where (62 ± 2)% of the regenerated inventory and (69 ± 1)% of the preformed inventory first reemerge into the euphotic zone.
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A Non-Abelian Geometric Phase for Spin Systems
NASA Astrophysics Data System (ADS)
H M, Bharath; Boguslawski, Matthew; Barrios, Maryrose; Chapman, Michael
Berry's geometric phase has been used to characterize topological phase transitions. Recent works have addressed the question of whether generalizations of Berry's phase to mixed states can be used to characterize topological phase transitions. Berry's phase is essentially the geometric information stored in the overall phase of a quantum system. Here, we show that geometric information is also stored in the higher order spin moments of a quantum spin system. In particular, we show that when the spin vector of a quantum spin system with a spin 1 or higher is transported along a closed path inside the Bloch ball, the tensor of second moments picks up a geometric phase in the form of an SO(3) operator. Geometrically interpreting this phase is tantamount to defining a steradian angle for closed paths inside the Bloch ball. Typically the steradian angle is defined by projecting the path onto the surface of the Bloch ball. However, paths that pass through the center cannot be projected onto the surface. We show that the steradian angles of all paths, including those that pass through the center can be defined by projecting them onto a real projective plane, instead of a sphere. This steradian angle is equal to the geometric phase picked up by a spin system.
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Takayanagi, Toshiyuki; Nakatomi, Taiki; Yonetani, Yoshiteru
2018-04-20
We performed reaction path search calculations for the NaCl·(H 2 O) 6 cluster using the global reaction route mapping (GRRM) code to understand the atomic-level mechanisms of the NaCl → Na + + Cl - ionic dissociation induced by water solvents. Low-lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the NaCl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7-3.7 Å and that the NaCl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
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NASA Astrophysics Data System (ADS)
Cano-Lozano, José Carlos; Martínez-Bazán, Carlos; Magnaudet, Jacques; Tchoufag, Joël
2016-09-01
We report on a series of results provided by three-dimensional numerical simulations of nearly spheroidal bubbles freely rising and deforming in a still liquid in the regime close to the transition to path instability. These results improve upon those of recent computational studies [Cano-Lozano et al., Int. J. Multiphase Flow 51, 11 (2013), 10.1016/j.ijmultiphaseflow.2012.11.005; Phys. Fluids 28, 014102 (2016), 10.1063/1.4939703] in which the neutral curve associated with this transition was obtained by considering realistic but frozen bubble shapes. Depending on the dimensionless parameters that characterize the system, various paths geometries are observed by letting an initially spherical bubble starting from rest rise under the effect of buoyancy and adjust its shape to the surrounding flow. These include the well-documented rectilinear axisymmetric, planar zigzagging, and spiraling (or helical) regimes. A flattened spiraling regime that most often eventually turns into either a planar zigzagging or a helical regime is also frequently observed. Finally, a chaotic regime in which the bubble experiences small horizontal displacements (typically one order of magnitude smaller than in the other regimes) is found to take place in a region of the parameter space where no standing eddy exists at the back of the bubble. The discovery of this regime provides evidence that path instability does not always result from a wake instability as previously believed. In each regime, we examine the characteristics of the path, bubble shape, and vortical structure in the wake, as well as their couplings. In particular, we observe that, depending on the fluctuations of the rise velocity, two different vortex shedding modes exist in the zigzagging regime, confirming earlier findings with falling spheres. The simulations also reveal that significant bubble deformations may take place along zigzagging or spiraling paths and that, under certain circumstances, they dramatically alter the wake structure. The instability thresholds that can be inferred from the computations compare favorably with experimental data provided by various sets of recent experiments guaranteeing that the bubble surface is free of surfactants.
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Quantum circuit dynamics via path integrals: Is there a classical action for discrete-time paths?
NASA Astrophysics Data System (ADS)
Penney, Mark D.; Enshan Koh, Dax; Spekkens, Robert W.
2017-07-01
It is straightforward to compute the transition amplitudes of a quantum circuit using the sum-over-paths methodology when the gates in the circuit are balanced, where a balanced gate is one for which all non-zero transition amplitudes are of equal magnitude. Here we consider the question of whether, for such circuits, the relative phases of different discrete-time paths through the configuration space can be defined in terms of a classical action, as they are for continuous-time paths. We show how to do so for certain kinds of quantum circuits, namely, Clifford circuits where the elementary systems are continuous-variable systems or discrete systems of odd-prime dimension. These types of circuit are distinguished by having phase-space representations that serve to define their classical counterparts. For discrete systems, the phase-space coordinates are also discrete variables. We show that for each gate in the generating set, one can associate a symplectomorphism on the phase-space and to each of these one can associate a generating function, defined on two copies of the configuration space. For discrete systems, the latter association is achieved using tools from algebraic geometry. Finally, we show that if the action functional for a discrete-time path through a sequence of gates is defined using the sum of the corresponding generating functions, then it yields the correct relative phases for the path-sum expression. These results are likely to be relevant for quantizing physical theories where time is fundamentally discrete, characterizing the classical limit of discrete-time quantum dynamics, and proving complexity results for quantum circuits.
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REVIEWS OF TOPICAL PROBLEMS: Transition radiation in media with random inhomogeneities
NASA Astrophysics Data System (ADS)
Platonov, Konstantin Yu; Fleishman, G. D.
2002-03-01
This review analyzes radiation produced by randomly inhomogeneous media excited by fast particles — i.e., polarization bremsstrahlung for thermodynamically equilibrium inhomogeneities or transition radiation for nonthermal ones — taking into account all the effects important for natural sources. Magnetic field effects on both the motion of fast particles and the dispersion of background plasma are considered, and the multiple scattering of fast particles in the medium is examined. Various resonant effects occurring under the conditions of Cherenkov (or cyclotron) emission for a particular eigenmode are discussed. The transition radiation intensity and absorption (amplification) coefficients are calculated for ensembles of fast particles with realistic distributions over momentum and angles. The value of the developed theory of transition radiation is illustrated by applying it to astrophysical objects. Transition radiation is shown to contribute significantly to the radio emission of the Sun, planets (including Earth), and interplanetary and interstellar media. Possible further applications of transition radiation (particularly stimulated) are discussed.
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Towards a critical transition theory under different temporal scales and noise strengths
NASA Astrophysics Data System (ADS)
Shi, Jifan; Li, Tiejun; Chen, Luonan
2016-03-01
The mechanism of critical phenomena or critical transitions has been recently studied from various aspects, in particular considering slow parameter change and small noise. In this article, we systematically classify critical transitions into three types based on temporal scales and noise strengths of dynamical systems. Specifically, the classification is made by comparing three important time scales τλ, τtran, and τergo, where τλ is the time scale of parameter change (e.g., the change of environment), τtran is the time scale when a particle or state transits from a metastable state into another, and τergo is the time scale when the system becomes ergodic. According to the time scales, we classify the critical transition behaviors as three types, i.e., state transition, basin transition, and distribution transition. Moreover, for each type of transition, there are two cases, i.e., single-trajectory transition and multitrajectory ensemble transition, which correspond to the transition of individual behavior and population behavior, respectively. We also define the critical point for each type of critical transition, derive several properties, and further propose the indicators for predicting critical transitions with numerical simulations. In addition, we show that the noise-to-signal ratio is effective to make the classification of critical transitions for real systems.
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Exploring the Dynamics of Transit Times and Subsurface Mixing in a Small Agricultural Catchment
NASA Astrophysics Data System (ADS)
Yang, Jie; Heidbüchel, Ingo; Musolff, Andreas; Reinstorf, Frido; Fleckenstein, Jan H.
2018-03-01
The analysis of transit/residence time distributions (TTDs and RTDs) provides important insights into the dynamics of stream-water ages and subsurface mixing. These insights have significant implications for water quality. For a small agricultural catchment in central Germany, we use a 3D fully coupled surface-subsurface hydrological model to simulate water flow and perform particle tracking to determine flow paths and transit times. The TTDs of discharge, RTDs of storage and fractional StorAge Selection (fSAS) functions are computed and analyzed on daily basis for a period of 10 years. Results show strong seasonal fluctuations of the median transit time of discharge and the median residence time, with the former being strongly related to the catchment wetness. Computed fSAS functions suggest systematic shifts of the discharge selection preference over four main periods: In the wet period, the youngest water in storage is preferentially selected, and this preference shifts gradually toward older ages of stored water when the catchment transitions into the drying, dry and wetting periods. These changes are driven by distinct shifts in the dominance of deeper flow paths and fast shallow flow paths. Changes in the shape of the fSAS functions can be captured by changes in the two parameters of the approximating Beta distributions, allowing the generation of continuous fSAS functions representing the general catchment behavior. These results improve our understanding of the seasonal dynamics of TTDs and fSAS functions for a complex real-world catchment and are important for interpreting solute export to the stream in a spatially implicit manner.
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Nonlinear problems in data-assimilation : Can synchronization help?
NASA Astrophysics Data System (ADS)
Tribbia, J. J.; Duane, G. S.
2009-12-01
Over the past several years, operational weather centers have initiated ensemble prediction and assimilation techniques to estimate the error covariance of forecasts in the short and the medium range. The ensemble techniques used are based on linear methods. The theory This technique s been shown to be a useful indicator of skill in the linear range where forecast errors are small relative to climatological variance. While this advance has been impressive, there are still ad hoc aspects of its use in practice, like the need for covariance inflation which are troubling. Furthermore, to be of utility in the nonlinear range an ensemble assimilation and prediction method must be capable of giving probabilistic information for the situation where a probability density forecast becomes multi-modal. A prototypical, simplest example of such a situation is the planetary-wave regime transition where the pdf is bimodal. Our recent research show how the inconsistencies and extensions of linear methodology can be consistently treated using the paradigm of synchronization which views the problems of assimilation and forecasting as that of optimizing the forecast model state with respect to the future evolution of the atmosphere.
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Nanostructured complex oxides as a route towards thermal behavior in artificial spin ice systems
NASA Astrophysics Data System (ADS)
Chopdekar, R. V.; Li, B.; Wynn, T. A.; Lee, M. S.; Jia, Y.; Liu, Z. Q.; Biegalski, M. D.; Retterer, S. T.; Young, A. T.; Scholl, A.; Takamura, Y.
2017-07-01
We have used soft x-ray photoemission electron microscopy to image the magnetization of single-domain L a0.7S r0.3Mn O3 nanoislands arranged in geometrically frustrated configurations such as square ice and kagome ice geometries. Upon thermal randomization, ensembles of nanoislands with strong interisland magnetic coupling relax towards low-energy configurations. Statistical analysis shows that the likelihood of ensembles falling into low-energy configurations depends strongly on the annealing temperature. Annealing to just below the Curie temperature of the ferromagnetic film (TC=338 K ) allows for a much greater probability of achieving low-energy configurations as compared to annealing above the Curie temperature. At this thermally active temperature of 325 K, the ensemble of ferromagnetic nanoislands explore their energy landscape over time and eventually transition to lower energy states as compared to the frozen-in configurations obtained upon cooling from above the Curie temperature. Thus, this materials system allows for a facile method to systematically study thermal evolution of artificial spin ice arrays of nanoislands at temperatures modestly above room temperature.
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Multiensemble Markov models of molecular thermodynamics and kinetics.
Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank
2016-06-07
We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model.
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Multiensemble Markov models of molecular thermodynamics and kinetics
Wu, Hao; Paul, Fabian; Noé, Frank
2016-01-01
We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302
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Weighted projected networks: mapping hypergraphs to networks.
López, Eduardo
2013-05-01
Many natural, technological, and social systems incorporate multiway interactions, yet are characterized and measured on the basis of weighted pairwise interactions. In this article, I propose a family of models in which pairwise interactions originate from multiway interactions, by starting from ensembles of hypergraphs and applying projections that generate ensembles of weighted projected networks. I calculate analytically the statistical properties of weighted projected networks, and suggest ways these could be used beyond theoretical studies. Weighted projected networks typically exhibit weight disorder along links even for very simple generating hypergraph ensembles. Also, as the size of a hypergraph changes, a signature of multiway interaction emerges on the link weights of weighted projected networks that distinguishes them from fundamentally weighted pairwise networks. This signature could be used to search for hidden multiway interactions in weighted network data. I find the percolation threshold and size of the largest component for hypergraphs of arbitrary uniform rank, translate the results into projected networks, and show that the transition is second order. This general approach to network formation has the potential to shed new light on our understanding of weighted networks.
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Phase Transitions in a Model of Y-Molecules Abstract
NASA Astrophysics Data System (ADS)
Holz, Danielle; Ruth, Donovan; Toral, Raul; Gunton, James
Immunoglobulin is a Y-shaped molecule that functions as an antibody to neutralize pathogens. In special cases where there is a high concentration of immunoglobulin molecules, self-aggregation can occur and the molecules undergo phase transitions. This prevents the molecules from completing their function. We used a simplified model of 2-Dimensional Y-molecules with three identical arms on a triangular lattice with 2-dimensional Grand Canonical Ensemble. The molecules were permitted to be placed, removed, rotated or moved on the lattice. Once phase coexistence was found, we used histogram reweighting and multicanonical sampling to calculate our phase diagram.
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Order parameter analysis of synchronization transitions on star networks
NASA Astrophysics Data System (ADS)
Chen, Hong-Bin; Sun, Yu-Ting; Gao, Jian; Xu, Can; Zheng, Zhi-Gang
2017-12-01
The collective behaviors of populations of coupled oscillators have attracted significant attention in recent years. In this paper, an order parameter approach is proposed to study the low-dimensional dynamical mechanism of collective synchronizations, by adopting the star-topology of coupled oscillators as a prototype system. The order parameter equation of star-linked phase oscillators can be obtained in terms of the Watanabe-Strogatz transformation, Ott-Antonsen ansatz, and the ensemble order parameter approach. Different solutions of the order parameter equation correspond to the diverse collective states, and different bifurcations reveal various transitions among these collective states. The properties of various transitions in the star-network model are revealed by using tools of nonlinear dynamics such as time reversibility analysis and linear stability analysis.
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Statistical crossover characterization of the heterotic localized-extended transition.
Ugajin, Ryuichi
2003-07-01
We investigated the spectral statistics of a quantum particle in a superlattice consisting of a disordered layer and a clean layer, possibly accompanied by random magnetic fields. Because a disordered layer has localized states and a clean layer has extended states, our quantum system shows a heterotic phase of an Anderson insulator and a normal metal. As the ratio of the volume of these two layers changes, the spectral statistics change from Poissonian to one of the Gaussian ensembles which characterize quantum chaos. A crossover distribution specified by two parameters is introduced to distinguish the transition from an integrable system to a quantum chaotic system during the heterotic phase from an Anderson transition in which the degree of random potentials is homogenous.
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NASA Astrophysics Data System (ADS)
Ou, Jiemei; Yang, Yuzhao; Lin, Wensheng; Yuan, Zhongke; Gan, Lin; Lin, Xiaofeng; Chen, Xudong; Chen, Yujie
2015-03-01
We investigated the transitions of conformations and their effects on emission properties of poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) single molecules in PMMA matrix during thermal annealing process. Total internal reflection fluorescence microscopy measurements reveal the transformation from collapsed conformations to extended, highly ordered rod-like structures of MEH-PPV single molecules during thermal annealing. The blue shifts in the ensemble single molecule PL spectra support our hypnosis. The transition occurs as the annealing temperature exceeds 100 °C, implying that an annealing temperature near the glass transition temperature Tg of matrix is ideal for the control and optimization of blend polymer films.
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Kearns, William D; Fozard, James L; Ray, Roger D; Scott, Steven; Jasiewicz, Jan M; Craighead, Jeffrey D; Pagano, Craig V
2016-01-01
Rehabilitation of patients with traumatic brain injury typically includes therapeutic prompts for keeping appointments and adhering to medication regimens. Level of cognitive impairment may significantly affect a traumatic brain injury victim's ability to benefit from text-based prompting. We tested the hypothesis that spatial disorientation as measured by movement path tortuosity during ambulation would be associated with poorer compliance with automated prompts by veterans actively being treated for traumatic brain injury. Clinical polytrauma center. Ten (1 female) veteran patients mean age = 35.4 (SD = 12.4) years. Small group correlational study without random assignment. Fractal Dimension, a measure of movement path tortuosity derived from a GPS logging device used to record casual outdoor ambulation at the start of the study. Compliance with smart home machine-generated therapeutic prompts received during rehabilitation at the James A. Haley Veterans Administration Hospital Polytrauma Transitional Rehabilitation Program. A patient was compliant with a prompt if they transited from where the prompt was presented to the prescribed destination (both within the Polytrauma Transitional Rehabilitation Program) within 30 minutes. Noncompliance was failure to appear at the destination within the allotted time. Fractal dimension was significantly inversely related to overall prompt compliance (r = -0.603, n = 10, P = .032; 1-tailed). The findings support the hypothesis that increased spatial disorientation adversely impacts compliance with automated prompts throughout therapy. The results are consistent with previous studies linking elevated path tortuosity to cognitive impairment and increased risk for falls in assisted living facility residents.
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Ohta, Yoshihiro; Nishiyama, Akinobu; Wada, Yoichiro; Ruan, Yijun; Kodama, Tatsuhiko; Tsuboi, Takashi; Tokihiro, Tetsuji; Ihara, Sigeo
2012-08-01
We all use path routing everyday as we take shortcuts to avoid traffic jams, or by using faster traffic means. Previous models of traffic flow of RNA polymerase II (RNAPII) during transcription, however, were restricted to one dimension along the DNA template. Here we report the modeling and application of traffic flow in transcription that allows preferential paths of different dimensions only restricted to visit some transit points, as previously introduced between the 5' and 3' end of the gene. According to its position, an RNAPII protein molecule prefers paths obeying two types of time-evolution rules. One is an asymmetric simple exclusion process (ASEP) along DNA, and the other is a three-dimensional jump between transit points in DNA where RNAPIIs are staying. Simulations based on our model, and comparison experimental results, reveal how RNAPII molecules are distributed at the DNA-loop-formation-related protein binding sites as well as CTCF insulator proteins (or exons). As time passes after the stimulation, the RNAPII density at these sites becomes higher. Apparent far-distance jumps in one dimension are realized by short-range three-dimensional jumps between DNA loops. We confirm the above conjecture by applying our model calculation to the SAMD4A gene by comparing the experimental results. Our probabilistic model provides possible scenarios for assembling RNAPII molecules into transcription factories, where RNAPII and related proteins cooperatively transcribe DNA.
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Transitional Patterns of Adolescent Females in Non-Traditional Career Paths.
ERIC Educational Resources Information Center
Ciccocioppo, Anna-Lisa; Stewin, Leonard L.; Madill, Helen M.; Montgomerie, T. Craig; Tovell, Dorothy R.; Armour, Margaret-Ann; Fitzsimmons, George W.
2002-01-01
Examines the factors that affected the career decision-making of adolescent females and young women in undergraduate science, engineering, and technology programs. Qualitative analysis was used to uncover seven themes: transition from high school, educational influences, family influences, academic issues, coursework management, gender issues, and…
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The Bulgarian Academic Profession in Transition.
ERIC Educational Resources Information Center
Slantcheva, Snejana
2003-01-01
Analyzes the current status of the academic profession in Bulgaria at a time of difficult socioeconomic transition. After providing a brief overview of the historical development of Bulgarian academia, discusses faculty working conditions, the career path within the profession, and the legal framework for the professoriate. Highlights future key…
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Scan path entropy and arrow plots: capturing scanning behavior of multiple observers
Hooge, Ignace; Camps, Guido
2013-01-01
Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures (1) “scan path entropy” to quantify gaze guidance and (2) the “arrow plot” to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50). The new measures were tested in an eye tracking study (48 observers, 39 advertisements). Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place. PMID:24399993
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USDA-ARS?s Scientific Manuscript database
Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...
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NASA Astrophysics Data System (ADS)
Kim, Minkyu; Chang, Jaeeon; Sandler, Stanley I.
2014-02-01
Accurate values of the free energies of C60 and C70 fullerene crystals are obtained using expanded ensemble method and acceptance ratio method combined with the Einstein-molecule approach. Both simulation methods, when tested for Lennard-Jones crystals, give accurate results of the free energy differing from each other in the fifth significant digit. The solid-solid phase transition temperature of C60 crystal is determined from free energy profiles, and found to be 260 K, which is in good agreement with experiment. For C70 crystal, using the potential model of Sprik et al. [Phys. Rev. Lett. 69, 1660 (1992)], low-temperature solid-solid phase transition temperature is found to be 160 K determined from the free energy profiles. Whereas this is somewhat lower than the experimental value, it is in agreement with conventional molecular simulations, which validates the methodological consistency of the present simulation method. From the calculations of the free energies of C60 and C70 crystals, we note the significance of symmetry number for crystal phase needed to properly account for the indistinguishability of orientationally disordered states.
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Modelling machine ensembles with discrete event dynamical system theory
NASA Technical Reports Server (NTRS)
Hunter, Dan
1990-01-01
Discrete Event Dynamical System (DEDS) theory can be utilized as a control strategy for future complex machine ensembles that will be required for in-space construction. The control strategy involves orchestrating a set of interactive submachines to perform a set of tasks for a given set of constraints such as minimum time, minimum energy, or maximum machine utilization. Machine ensembles can be hierarchically modeled as a global model that combines the operations of the individual submachines. These submachines are represented in the global model as local models. Local models, from the perspective of DEDS theory , are described by the following: a set of system and transition states, an event alphabet that portrays actions that takes a submachine from one state to another, an initial system state, a partial function that maps the current state and event alphabet to the next state, and the time required for the event to occur. Each submachine in the machine ensemble is presented by a unique local model. The global model combines the local models such that the local models can operate in parallel under the additional logistic and physical constraints due to submachine interactions. The global model is constructed from the states, events, event functions, and timing requirements of the local models. Supervisory control can be implemented in the global model by various methods such as task scheduling (open-loop control) or implementing a feedback DEDS controller (closed-loop control).
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Chirikjian, Gregory S.
2011-01-01
Proteins fold from a highly disordered state into a highly ordered one. Traditionally, the folding problem has been stated as one of predicting ‘the’ tertiary structure from sequential information. However, new evidence suggests that the ensemble of unfolded forms may not be as disordered as once believed, and that the native form of many proteins may not be described by a single conformation, but rather an ensemble of its own. Quantifying the relative disorder in the folded and unfolded ensembles as an entropy difference may therefore shed light on the folding process. One issue that clouds discussions of ‘entropy’ is that many different kinds of entropy can be defined: entropy associated with overall translational and rotational Brownian motion, configurational entropy, vibrational entropy, conformational entropy computed in internal or Cartesian coordinates (which can even be different from each other), conformational entropy computed on a lattice; each of the above with different solvation and solvent models; thermodynamic entropy measured experimentally, etc. The focus of this work is the conformational entropy of coil/loop regions in proteins. New mathematical modeling tools for the approximation of changes in conformational entropy during transition from unfolded to folded ensembles are introduced. In particular, models for computing lower and upper bounds on entropy for polymer models of polypeptide coils both with and without end constraints are presented. The methods reviewed here include kinematics (the mathematics of rigid-body motions), classical statistical mechanics and information theory. PMID:21187223
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Schweiner, Frank; Laturner, Jeanine; Main, Jörg; Wunner, Günter
2017-11-01
Until now only for specific crossovers between Poissonian statistics (P), the statistics of a Gaussian orthogonal ensemble (GOE), or the statistics of a Gaussian unitary ensemble (GUE) have analytical formulas for the level spacing distribution function been derived within random matrix theory. We investigate arbitrary crossovers in the triangle between all three statistics. To this aim we propose an according formula for the level spacing distribution function depending on two parameters. Comparing the behavior of our formula for the special cases of P→GUE, P→GOE, and GOE→GUE with the results from random matrix theory, we prove that these crossovers are described reasonably. Recent investigations by F. Schweiner et al. [Phys. Rev. E 95, 062205 (2017)2470-004510.1103/PhysRevE.95.062205] have shown that the Hamiltonian of magnetoexcitons in cubic semiconductors can exhibit all three statistics in dependence on the system parameters. Evaluating the numerical results for magnetoexcitons in dependence on the excitation energy and on a parameter connected with the cubic valence band structure and comparing the results with the formula proposed allows us to distinguish between regular and chaotic behavior as well as between existent or broken antiunitary symmetries. Increasing one of the two parameters, transitions between different crossovers, e.g., from the P→GOE to the P→GUE crossover, are observed and discussed.
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An Optimization Principle for Deriving Nonequilibrium Statistical Models of Hamiltonian Dynamics
NASA Astrophysics Data System (ADS)
Turkington, Bruce
2013-08-01
A general method for deriving closed reduced models of Hamiltonian dynamical systems is developed using techniques from optimization and statistical estimation. Given a vector of resolved variables, selected to describe the macroscopic state of the system, a family of quasi-equilibrium probability densities on phase space corresponding to the resolved variables is employed as a statistical model, and the evolution of the mean resolved vector is estimated by optimizing over paths of these densities. Specifically, a cost function is constructed to quantify the lack-of-fit to the microscopic dynamics of any feasible path of densities from the statistical model; it is an ensemble-averaged, weighted, squared-norm of the residual that results from submitting the path of densities to the Liouville equation. The path that minimizes the time integral of the cost function determines the best-fit evolution of the mean resolved vector. The closed reduced equations satisfied by the optimal path are derived by Hamilton-Jacobi theory. When expressed in terms of the macroscopic variables, these equations have the generic structure of governing equations for nonequilibrium thermodynamics. In particular, the value function for the optimization principle coincides with the dissipation potential that defines the relation between thermodynamic forces and fluxes. The adjustable closure parameters in the best-fit reduced equations depend explicitly on the arbitrary weights that enter into the lack-of-fit cost function. Two particular model reductions are outlined to illustrate the general method. In each example the set of weights in the optimization principle contracts into a single effective closure parameter.
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Spectral statistics of random geometric graphs
NASA Astrophysics Data System (ADS)
Dettmann, C. P.; Georgiou, O.; Knight, G.
2017-04-01
We use random matrix theory to study the spectrum of random geometric graphs, a fundamental model of spatial networks. Considering ensembles of random geometric graphs we look at short-range correlations in the level spacings of the spectrum via the nearest-neighbour and next-nearest-neighbour spacing distribution and long-range correlations via the spectral rigidity Δ3 statistic. These correlations in the level spacings give information about localisation of eigenvectors, level of community structure and the level of randomness within the networks. We find a parameter-dependent transition between Poisson and Gaussian orthogonal ensemble statistics. That is the spectral statistics of spatial random geometric graphs fits the universality of random matrix theory found in other models such as Erdős-Rényi, Barabási-Albert and Watts-Strogatz random graphs.
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The surgical ensemble: choreography as a simulation and training tool.
Satava, Richard M; Hunter, Anne Marie
2011-09-01
Team training and interprofessional training have recently emerged as critical new simulations that enhance performance by coordinating communication, leadership, professional, and, to a certain extent, technical skills. In describing these new training tools, the term choreography has been loosely used, but no critical appraisal of the role of the science of choreography has been applied to a surgical procedure. By analogy, the surgical team, including anesthetists, surgeons, nurses, and technicians, constitutes a complete ensemble, whose physical actions and interactions constitute the "performance of surgery." There are very specific "elements" (tools) that are basic to choreography, such as space, timing, rhythm, energy, cues, transitions, and especially rehearsal. This review explores whether such a metaphor is appropriate and the possibility of applying the science of choreography to the surgical team in the operating theater.
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NASA Astrophysics Data System (ADS)
Mulders, P. J.
2018-03-01
Light-front quantized quark and gluon states (partons) play a dominant role in high energy scattering processes. Initial state hadrons are mixed ensembles of partons, while produced pure partonic states appear as mixed ensembles of hadrons. The transition from collinear hard physics to the 3D structure including partonic transverse momenta is related to confinement which links color and spatial degrees of freedom. We outline ideas on emergent symmetries in the Standard Model and their connection to the 3D structure of hadrons. Wilson loops, including those with light-like Wilson lines such as used in the studies of transverse momentum dependent distribution functions may play a crucial role here, establishing a direct link between transverse spatial degrees of freedom and gluonic degrees of freedom.
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Localization in covariance matrices of coupled heterogenous Ornstein-Uhlenbeck processes
NASA Astrophysics Data System (ADS)
Barucca, Paolo
2014-12-01
We define a random-matrix ensemble given by the infinite-time covariance matrices of Ornstein-Uhlenbeck processes at different temperatures coupled by a Gaussian symmetric matrix. The spectral properties of this ensemble are shown to be in qualitative agreement with some stylized facts of financial markets. Through the presented model formulas are given for the analysis of heterogeneous time series. Furthermore evidence for a localization transition in eigenvectors related to small and large eigenvalues in cross-correlations analysis of this model is found, and a simple explanation of localization phenomena in financial time series is provided. Finally we identify both in our model and in real financial data an inverted-bell effect in correlation between localized components and their local temperature: high- and low-temperature components are the most localized ones.
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Hamiltonian mean-field model: effect of temporal perturbation in coupling matrix
NASA Astrophysics Data System (ADS)
Bhadra, Nivedita; Patra, Soumen K.
2018-05-01
The Hamiltonian mean-field (HMF) model is a system of fully coupled rotators which exhibits a second-order phase transition at some critical energy in its canonical ensemble. We investigate the case where the interaction between the rotors is governed by a time-dependent coupling matrix. Our numerical study reveals a shift in the critical point due to the temporal modulation. The shift in the critical point is shown to be independent of the modulation frequency above some threshold value, whereas the impact of the amplitude of modulation is dominant. In the microcanonical ensemble, the system with constant coupling reaches a quasi-stationary state (QSS) at an energy near the critical point. Our result indicates that the QSS subsists in presence of such temporal modulation of the coupling parameter.
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Bifurcations on Potential Energy Surfaces of Organic Reactions
Ess, Daniel H.; Wheeler, Steven E.; Iafe, Robert G.; Xu, Lai; Çelebi-Ölçüm, Nihan; Houk, K. N.
2009-01-01
A single transition state may lead to multiple intermediates or products if there is a post-transition state reaction path bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects control selectivity rather than transition state energetics. This minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions. PMID:18767086
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NASA Astrophysics Data System (ADS)
Guillot, T.; Santos, N. C.; Pont, F.; Iro, N.; Melo, C.; Ribas, I.
2006-07-01
Context.Nine extrasolar planets with masses between 110 and 430 M_⊕ are known to transit their star. The knowledge of their masses and radii allows an estimate of their composition, but uncertainties on equations of state, opacities and possible missing energy sources imply that only inaccurate constraints can be derived when considering each planet separately.Aims.We seek to better understand the composition of transiting extrasolar planets by considering them as an ensemble, and by comparing the obtained planetary properties to that of the parent stars.Methods.We use evolution models and constraints on the stellar ages to derive the mass of heavy elements present in the planets. Possible additional energy sources like tidal dissipation due to an inclined orbit or to downward kinetic energy transport are considered.Results.We show that the nine transiting planets discovered so far belong to a quite homogeneous ensemble that is characterized by a mass of heavy elements that is a relatively steep function of the stellar metallicity, from less than 20 earth masses of heavy elements around solar composition stars, to up to ~100 M_⊕ for three times the solar metallicity (the precise values being model-dependant). The correlation is still to be ascertained however. Statistical tests imply a worst-case 1/3 probability of a false positive.Conclusions.Together with the observed lack of giant planets in close orbits around metal-poor stars, these results appear to imply that heavy elements play a key role in the formation of close-in giant planets. The large masses of heavy elements inferred for planets orbiting metal rich stars was not anticipated by planet formation models and shows the need for alternative theories including migration and subsequent collection of planetesimals.
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Szathmáry, E
2000-01-01
Replicators of interest in chemistry, biology and culture are briefly surveyed from a conceptual point of view. Systems with limited heredity have only a limited evolutionary potential because the number of available types is too low. Chemical cycles, such as the formose reaction, are holistic replicators since replication is not based on the successive addition of modules. Replicator networks consisting of catalytic molecules (such as reflexively autocatalytic sets of proteins, or reproducing lipid vesicles) are hypothetical ensemble replicators, and their functioning rests on attractors of their dynamics. Ensemble replicators suffer from the paradox of specificity: while their abstract feasibility seems to require a high number of molecular types, the harmful effect of side reactions calls for a small system size. No satisfactory solution to this problem is known. Phenotypic replicators do not pass on their genotypes, only some aspects of the phenotype are transmitted. Phenotypic replicators with limited heredity include genetic membranes, prions and simple memetic systems. Memes in human culture are unlimited hereditary, phenotypic replicators, based on language. The typical path of evolution goes from limited to unlimited heredity, and from attractor-based to modular (digital) replicators. PMID:11127914
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Szathmáry, E
2000-11-29
Replicators of interest in chemistry, biology and culture are briefly surveyed from a conceptual point of view. Systems with limited heredity have only a limited evolutionary potential because the number of available types is too low. Chemical cycles, such as the formose reaction, are holistic replicators since replication is not based on the successive addition of modules. Replicator networks consisting of catalytic molecules (such as reflexively autocatalytic sets of proteins, or reproducing lipid vesicles) are hypothetical ensemble replicators, and their functioning rests on attractors of their dynamics. Ensemble replicators suffer from the paradox of specificity: while their abstract feasibility seems to require a high number of molecular types, the harmful effect of side reactions calls for a small system size. No satisfactory solution to this problem is known. Phenotypic replicators do not pass on their genotypes, only some aspects of the phenotype are transmitted. Phenotypic replicators with limited heredity include genetic membranes, prions and simple memetic systems. Memes in human culture are unlimited hereditary, phenotypic replicators, based on language. The typical path of evolution goes from limited to unlimited heredity, and from attractor-based to modular (digital) replicators.
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NASA Technical Reports Server (NTRS)
Jahshan, S. N.; Singleterry, R. C.
2001-01-01
The effect of random fuel redistribution on the eigenvalue of a one-speed reactor is investigated. An ensemble of such reactors that are identical to a homogeneous reference critical reactor except for the fissile isotope density distribution is constructed such that it meets a set of well-posed redistribution requirements. The average eigenvalue,
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Genome-scale modeling of the evolutionary path to C4 photosynthesis
NASA Astrophysics Data System (ADS)
Myers, Christopher R.; Bogart, Eli
In C4 photosynthesis, plants maintain a high carbon dioxide level in specialized bundle sheath cells surrounding leaf veins and restrict CO2 assimilation to those cells, favoring CO2 over O2 in competition for Rubisco active sites. In C3 plants, which do not possess such a carbon concentrating mechanism, CO2 fixation is reduced due to this competition. Despite the complexity of the C4 system, it has evolved convergently from more than 60 independent origins in diverse families of plants around the world over the last 30 million years. We study the evolution of the C4 system in a genome-scale model of plant metabolism that describes interacting mesophyll and bundle sheath cells and enforces key nonlinear kinetic relationships. Adapting the zero-temperature string method for simulating transition paths in physics and chemistry, we find the highest-fitness paths connecting C3 and C4 positions in the model's high-dimensional parameter space, and show that they reproduce known aspects of the C3-C4 transition while making additional predictions about metabolic changes along the path. We explore the relationship between evolutionary history and C4 biochemical subtype, and the effects of atmospheric carbon dioxide levels.
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MEPSA: minimum energy pathway analysis for energy landscapes.
Marcos-Alcalde, Iñigo; Setoain, Javier; Mendieta-Moreno, Jesús I; Mendieta, Jesús; Gómez-Puertas, Paulino
2015-12-01
From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: pagomez@cbm.csic.es. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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NASA Astrophysics Data System (ADS)
Zima, V. G.; Fedoruk, S. O.
1999-11-01
The transition amplitude is obtained for a free massive particle of arbitrary spin by calculating the path integral in the index-spinor formulation within the BFV-BRST approach. No renormalizations of the path integral measure were applied. The calculation has given the Weinberg propagator written in the index-free form by the use of an index spinor. The choice of boundary conditions on the index spinor determines the holomorphic or antiholomorphic representation for the canonical description of particle/antiparticle spin.
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Survey of Retired Military Pharmacist's Transition to a Civilian Pharmacy Career Path.
Bennett, David; Wellman, Greg; Mahmood, Maysaa; Freye, Ryan; Remund, Daniel; Samples, Phil L
2015-12-01
To explore variables relevant to transition to civilian pharmacy career path for retiring military pharmacists. A cross-sectional survey was designed to collect information from retired military pharmacists including demographics, military service information, postretirement employment and perceptions of transition, satisfaction, level of responsibility, work environment, rewards (level of financial compensation, opportunities for professional development and career advancement, health benefits), and level of supervisory support. The questionnaire also included additional items asking about their perception of their military experience, transition to civilian work and the impact the military career had on their personal and family life. Respondents included 140 retired pharmacists from the U.S. Army, Navy, Air Force, or Coast Guard. Factors found to be significant predictors of transition to civilian career included: bureaucracy in current job, time elapsed since retirement, extent to which an individual misses military structure and chain of command, access to military facilities and Veterans Administration benefits, and reporting little or no stress in committed long-term personal relationship while in the military. Findings suggest that the majority of retired military pharmacists perceived the transition to civilian professional sector was about what they expected or easier than expected. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.
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Verification of Meteorological and Oceanographic Ensemble Forecasts in the U.S. Navy
NASA Astrophysics Data System (ADS)
Klotz, S.; Hansen, J.; Pauley, P.; Sestak, M.; Wittmann, P.; Skupniewicz, C.; Nelson, G.
2013-12-01
The Navy Ensemble Forecast Verification System (NEFVS) has been promoted recently to operational status at the U.S. Navy's Fleet Numerical Meteorology and Oceanography Center (FNMOC). NEFVS processes FNMOC and National Centers for Environmental Prediction (NCEP) meteorological and ocean wave ensemble forecasts, gridded forecast analyses, and innovation (observational) data output by FNMOC's data assimilation system. The NEFVS framework consists of statistical analysis routines, a variety of pre- and post-processing scripts to manage data and plot verification metrics, and a master script to control application workflow. NEFVS computes metrics that include forecast bias, mean-squared error, conditional error, conditional rank probability score, and Brier score. The system also generates reliability and Receiver Operating Characteristic diagrams. In this presentation we describe the operational framework of NEFVS and show examples of verification products computed from ensemble forecasts, meteorological observations, and forecast analyses. The construction and deployment of NEFVS addresses important operational and scientific requirements within Navy Meteorology and Oceanography. These include computational capabilities for assessing the reliability and accuracy of meteorological and ocean wave forecasts in an operational environment, for quantifying effects of changes and potential improvements to the Navy's forecast models, and for comparing the skill of forecasts from different forecast systems. NEFVS also supports the Navy's collaboration with the U.S. Air Force, NCEP, and Environment Canada in the North American Ensemble Forecast System (NAEFS) project and with the Air Force and the National Oceanic and Atmospheric Administration (NOAA) in the National Unified Operational Prediction Capability (NUOPC) program. This program is tasked with eliminating unnecessary duplication within the three agencies, accelerating the transition of new technology, such as multi-model ensemble forecasting, to U.S. Department of Defense use, and creating a superior U.S. global meteorological and oceanographic prediction capability. Forecast verification is an important component of NAEFS and NUOPC. Distribution Statement A: Approved for Public Release; distribution is unlimited
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Verification of Meteorological and Oceanographic Ensemble Forecasts in the U.S. Navy
NASA Astrophysics Data System (ADS)
Klotz, S. P.; Hansen, J.; Pauley, P.; Sestak, M.; Wittmann, P.; Skupniewicz, C.; Nelson, G.
2012-12-01
The Navy Ensemble Forecast Verification System (NEFVS) has been promoted recently to operational status at the U.S. Navy's Fleet Numerical Meteorology and Oceanography Center (FNMOC). NEFVS processes FNMOC and National Centers for Environmental Prediction (NCEP) meteorological and ocean wave ensemble forecasts, gridded forecast analyses, and innovation (observational) data output by FNMOC's data assimilation system. The NEFVS framework consists of statistical analysis routines, a variety of pre- and post-processing scripts to manage data and plot verification metrics, and a master script to control application workflow. NEFVS computes metrics that include forecast bias, mean-squared error, conditional error, conditional rank probability score, and Brier score. The system also generates reliability and Receiver Operating Characteristic diagrams. In this presentation we describe the operational framework of NEFVS and show examples of verification products computed from ensemble forecasts, meteorological observations, and forecast analyses. The construction and deployment of NEFVS addresses important operational and scientific requirements within Navy Meteorology and Oceanography (METOC). These include computational capabilities for assessing the reliability and accuracy of meteorological and ocean wave forecasts in an operational environment, for quantifying effects of changes and potential improvements to the Navy's forecast models, and for comparing the skill of forecasts from different forecast systems. NEFVS also supports the Navy's collaboration with the U.S. Air Force, NCEP, and Environment Canada in the North American Ensemble Forecast System (NAEFS) project and with the Air Force and the National Oceanic and Atmospheric Administration (NOAA) in the National Unified Operational Prediction Capability (NUOPC) program. This program is tasked with eliminating unnecessary duplication within the three agencies, accelerating the transition of new technology, such as multi-model ensemble forecasting, to U.S. Department of Defense use, and creating a superior U.S. global meteorological and oceanographic prediction capability. Forecast verification is an important component of NAEFS and NUOPC.
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Men, Yumei; Yan, Qingzhao; Jiang, Guangfeng; Zhang, Xianren; Wang, Wenchuan
2009-05-01
In this work, we propose a method to stabilize a nucleus in the framework of lattice density-functional theory (LDFT) by imposing a suitable constraint. Using this method, the shape of critical nucleus and height of the nucleation barrier can be determined without using a predefined nucleus as input. As an application of this method, we study the nucleation behavior of vapor-liquid transition in nanosquare pores with infinite length and relate the observed hysteresis loop on an adsorption isotherm to the nucleation mechanism. According to the dependence of hysteresis and the nucleation mechanism on the fluid-wall interaction, w , in this work, we have classified w into three regions ( w>0.9 , 0.1< or =w< or =0.9 , and w<0.1 ), which are denoted as strongly, moderately, and weakly attractive fluid-wall interaction, respectively. The dependence of hysteresis on the fluid-wall interaction is interpreted by the different nucleation mechanisms. Our constrained LDFT calculations also show that the different transition paths may induce different nucleation behaviors. The transition path dependence should be considered if morphological transition of nuclei exists during a nucleation process.
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Kota, V K B; Chavda, N D; Sahu, R
2006-04-01
Interacting many-particle systems with a mean-field one-body part plus a chaos generating random two-body interaction having strength lambda exhibit Poisson to Gaussian orthogonal ensemble and Breit-Wigner (BW) to Gaussian transitions in level fluctuations and strength functions with transition points marked by lambda = lambda c and lambda = lambda F, respectively; lambda F > lambda c. For these systems a theory for the matrix elements of one-body transition operators is available, as valid in the Gaussian domain, with lambda > lambda F, in terms of orbital occupation numbers, level densities, and an integral involving a bivariate Gaussian in the initial and final energies. Here we show that, using a bivariate-t distribution, the theory extends below from the Gaussian regime to the BW regime up to lambda = lambda c. This is well tested in numerical calculations for 6 spinless fermions in 12 single-particle states.
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Scalable hydrothermal synthesis of free-standing VO₂ nanowires in the M1 phase.
Horrocks, Gregory A; Singh, Sujay; Likely, Maliek F; Sambandamurthy, G; Banerjee, Sarbajit
2014-09-24
VO2 nanostructures derived from solution-phase methods are often plagued by broadened and relatively diminished metal-insulator transitions and adventitious doping due to imperfect control of stoichiometry. Here, we demonstrate a stepwise scalable hydrothermal and annealing route for obtaining VO2 nanowires exhibiting almost 4 orders of magnitude abrupt (within 1 °C) metal-insulator transitions. The prepared nanowires have been characterized across their structural and electronic phase transitions using single-nanowire Raman microprobe analysis, ensemble differential scanning calorimetry, and single-nanowire electrical transport measurements. The electrical band gap is determined to be 600 meV and is consistent with the optical band gap of VO2, and the narrowness of differential scanning calorimetry profiles indicates homogeneity of stoichiometry. The preparation of high-quality free-standing nanowires exhibiting pronounced metal-insulator transitions by a solution-phase process allows for scalability, further solution-phase processing, incorporation within nanocomposites, and integration onto arbitrary substrates.
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Signs and stability in higher-derivative gravity
NASA Astrophysics Data System (ADS)
Narain, Gaurav
2018-02-01
Perturbatively renormalizable higher-derivative gravity in four space-time dimensions with arbitrary signs of couplings has been considered. Systematic analysis of the action with arbitrary signs of couplings in Lorentzian flat space-time for no-tachyons, fixes the signs. Feynman + i𝜖 prescription for these signs further grants necessary convergence in path-integral, suppressing the field modes with large action. This also leads to a sensible wick rotation where quantum computation can be performed. Running couplings for these sign of parameters make the massive tensor ghost innocuous leading to a stable and ghost-free renormalizable theory in four space-time dimensions. The theory has a transition point arising from renormalization group (RG) equations, where the coefficient of R2 diverges without affecting the perturbative quantum field theory (QFT). Redefining this coefficient gives a better handle over the theory around the transition point. The flow equations push the flow of parameters across the transition point. The flow beyond the transition point is analyzed using the one-loop RG equations which shows that the regime beyond the transition point has unphysical properties: there are tachyons, the path-integral loses positive definiteness, Newton’s constant G becomes negative and large, and perturbative parameters become large. These shortcomings indicate a lack of completeness beyond the transition point and need of a nonperturbative treatment of the theory beyond the transition point.
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NASA Astrophysics Data System (ADS)
Dremov, V. V.; Ionov, G. V.; Sapozhnikov, F. A.; Smirnov, N. A.; Karavaev, A. V.; Vorobyova, M. A.; Ryzhkov, M. V.
2015-09-01
The present work is devoted to classical molecular dynamics investigation into microscopic mechanisms of the bcc-hcp transition in iron. The interatomic potential of EAM type used in the calculations was tested for the capability to reproduce ab initio data on energy evolution along the bcc-hcp transformation path (Burgers deformation + shuffe) and then used in the large-scale MD simulations. The large-scale simulations included constant volume deformation along the Burgers path to study the origin and nature of the plasticity, hydrostatic volume compression of defect free samples above the bcc to hcp transition threshold to observe the formation of new phase embryos, and the volume compression of samples containing screw dislocations to study the effect of the dislocations on the probability of the new phase critical embryo formation. The volume compression demonstrated high level of metastability. The transition starts at pressure much higher than the equilibrium one. Dislocations strongly affect the probability of the critical embryo formation and significantly reduce the onset pressure of transition. The dislocations affect also the resulting structure of the samples upon the transition. The formation of layered structure is typical for the samples containing the dislocations. The results of the simulations were compared with the in-situ experimental data on the mechanism of the bcc-hcp transition in iron.
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Guyett, Paul J; Gloss, Lisa M
2012-01-20
The H2A-H2B histone heterodimer folds via monomeric and dimeric kinetic intermediates. Within ∼5 ms, the H2A and H2B polypeptides associate in a nearly diffusion limited reaction to form a dimeric ensemble, denoted I₂ and I₂*, the latter being a subpopulation characterized by a higher content of nonnative structure (NNS). The I₂ ensemble folds to the native heterodimer, N₂, through an observable, first-order kinetic phase. To determine the regions of structure in the I₂ ensemble, we characterized 26 Ala mutants of buried hydrophobic residues, spanning the three helices of the canonical histone folds of H2A and H2B and the H2B C-terminal helix. All but one targeted residue contributed significantly to the stability of I₂, the transition state and N₂; however, only residues in the hydrophobic core of the dimer interface perturbed the I₂* population. Destabilization of I₂* correlated with slower folding rates, implying that NNS is not a kinetic trap but rather accelerates folding. The pattern of Φ values indicated that residues forming intramolecular interactions in the peripheral helices contributed similar stability to I₂ and N₂, but residues involved in intermolecular interactions in the hydrophobic core are only partially folded in I₂. These findings suggest a dimerize-then-rearrange model. Residues throughout the histone fold contribute to the stability of I₂, but after the rapid dimerization reaction, the hydrophobic core of the dimer interface has few fully native interactions. In the transition state leading to N₂, more native-like interactions are developed and nonnative interactions are rearranged. Copyright © 2011 Elsevier Ltd. All rights reserved.
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Moučka, Filip; Lísal, Martin; Škvor, Jiří; Jirsák, Jan; Nezbeda, Ivo; Smith, William R
2011-06-23
We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid phase, incorporating readily available data from thermochemical tables that are based on well-defined reference states. It performs simulations of the aqueous solution at a fixed number of water molecules, pressure, temperature, and specified overall electrolyte chemical potential. Insertion/deletion of ions to/from the system is implemented using fractional ions, which are coupled to the system via a coupling parameter λ that varies between 0 (no interaction between the fractional ions and the other particles in the system) and 1 (full interaction between the fractional ions and the other particles of the system). Transitions between λ-states are accepted with a probability following from the osmotic ensemble partition function. Biasing weights associated with the λ-states are used in order to efficiently realize transitions between them; these are determined by means of the Wang-Landau method. We also propose a novel scaling procedure for λ, which can be used for both nonpolarizable and polarizable models of aqueous electrolyte systems. The approach is readily extended to involve other solvents, multiple electrolytes, and species complexation reactions. The method is illustrated for NaCl, using SPC/E water and several force field models for NaCl from the literature, and the results are compared with experiment at ambient conditions. Good agreement is obtained for the chemical potential-concentration curve and the solubility prediction is reasonable. Future improvements to the predictions will require improved force field models.
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From the physics of interacting polymers to optimizing routes on the London Underground
Yeung, Chi Ho; Saad, David; Wong, K. Y. Michael
2013-01-01
Optimizing paths on networks is crucial for many applications, ranging from subway traffic to Internet communication. Because global path optimization that takes account of all path choices simultaneously is computationally hard, most existing routing algorithms optimize paths individually, thus providing suboptimal solutions. We use the physics of interacting polymers and disordered systems to analyze macroscopic properties of generic path optimization problems and derive a simple, principled, generic, and distributed routing algorithm capable of considering all individual path choices simultaneously. We demonstrate the efficacy of the algorithm by applying it to: (i) random graphs resembling Internet overlay networks, (ii) travel on the London Underground network based on Oyster card data, and (iii) the global airport network. Analytically derived macroscopic properties give rise to insightful new routing phenomena, including phase transitions and scaling laws, that facilitate better understanding of the appropriate operational regimes and their limitations, which are difficult to obtain otherwise. PMID:23898198
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From the physics of interacting polymers to optimizing routes on the London Underground.
Yeung, Chi Ho; Saad, David; Wong, K Y Michael
2013-08-20
Optimizing paths on networks is crucial for many applications, ranging from subway traffic to Internet communication. Because global path optimization that takes account of all path choices simultaneously is computationally hard, most existing routing algorithms optimize paths individually, thus providing suboptimal solutions. We use the physics of interacting polymers and disordered systems to analyze macroscopic properties of generic path optimization problems and derive a simple, principled, generic, and distributed routing algorithm capable of considering all individual path choices simultaneously. We demonstrate the efficacy of the algorithm by applying it to: (i) random graphs resembling Internet overlay networks, (ii) travel on the London Underground network based on Oyster card data, and (iii) the global airport network. Analytically derived macroscopic properties give rise to insightful new routing phenomena, including phase transitions and scaling laws, that facilitate better understanding of the appropriate operational regimes and their limitations, which are difficult to obtain otherwise.
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Path Flow Estimation Using Time Varying Coefficient State Space Model
NASA Astrophysics Data System (ADS)
Jou, Yow-Jen; Lan, Chien-Lun
2009-08-01
The dynamic path flow information is very crucial in the field of transportation operation and management, i.e., dynamic traffic assignment, scheduling plan, and signal timing. Time-dependent path information, which is important in many aspects, is nearly impossible to be obtained. Consequently, researchers have been seeking estimation methods for deriving valuable path flow information from less expensive traffic data, primarily link traffic counts of surveillance systems. This investigation considers a path flow estimation problem involving the time varying coefficient state space model, Gibbs sampler, and Kalman filter. Numerical examples with part of a real network of the Taipei Mass Rapid Transit with real O-D matrices is demonstrated to address the accuracy of proposed model. Results of this study show that this time-varying coefficient state space model is very effective in the estimation of path flow compared to time-invariant model.
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Ahalawat, Navjeet; Arora, Simran; Murarka, Rajesh K
2015-08-27
The human cluster determinant 4 (CD4), expressed primarily on the surface of T helper cells, serves as a coreceptor in T-cell receptor recognition of MHC II antigen complexes. Besides its cellular functions, CD4 serves as a primary receptor of human immunodeficiency virus (HIV) type 1. The cytoplasmic tail of CD4 (residues 402-419) is known to be involved in direct interaction with the HIV-1 proteins Vpu and Nef. These two viral accessory proteins (Vpu and Nef) downregulate CD4 in HIV-1 infected cells by multiple strategies and make the body susceptible to all forms of infections. In this work, we carried out extensive replica exchange molecular dynamics simulations in explicit water with three popular protein force fields Amber ff99SB, Amber ff99SB*-ILDN, and CHARMM36 to characterize the equilibrium conformational ensemble of CD4-tail (402-419) and further validated the simulated ensembles with known NMR data. We found that ff99SB*-ILDN gives a better description of the structural ensemble of this peptide compared with ff99SB and CHARMM36. The peptide adopts multiple distinct conformations with varying degree of residual secondary structures. In particular, we observed 28, 7, and 5% average α-helical, β-strand, and 3(10)-helix content, respectively, for ff99SB*-ILDN. The peptide chain shows the tendency of helix formation in a cooperative manner, seeding at residues 407-410, and subsequently extending toward both ends of the chain. Furthermore, we constructed Markov state model (MSM) from large-scale molecular dynamics simulations to study the dynamics of transitions between different metastable states explored by this peptide. The mean first passage times computed from MSM indicate rapid interconversion of these states, and the time scales of transitions range from several nanoseconds to hundreds of microseconds. Our results show good agreement with experimental data and could help to understand the key molecular mechanisms of T-cell activation and HIV-mediated receptor interference.
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Sobanska, M; Fernández-Garrido, S; Zytkiewicz, Z R; Tchutchulashvili, G; Gieraltowska, S; Brandt, O; Geelhaar, L
2016-08-12
We present a comprehensive description of the self-assembled nucleation and growth of GaN nanowires (NWs) by plasma-assisted molecular beam epitaxy on amorphous Al x O y buffers (a-Al x O y ) prepared by atomic layer deposition. The results are compared with those obtained on nitridated Si(111). Using line-of-sight quadrupole mass spectrometry, we analyze in situ the incorporation of Ga starting from the incubation and nucleation stages till the formation of the final nanowire ensemble and observe qualitatively the same time dependence for the two types of substrates. However, on a-Al x O y the incubation time is shorter and the nucleation faster than on nitridated Si. Moreover, on a-Al x O y we observe a novel effect of decrease in incorporated Ga flux for long growth durations which we explain by coalescence of NWs leading to reduction of the GaN surface area where Ga may reside. Dedicated samples are used to analyze the evolution of surface morphology. In particular, no GaN nuclei are detected when growth is interrupted during the incubation stage. Moreover, for a-Al x O y , the same shape transition from spherical cap-shaped GaN crystallites to the NW-like geometry is found as it is known for nitridated Si. However, while the critical radius for this transition is only slightly larger for a-Al x O y than for nitridated Si, the critical height is more than six times larger for a-Al x O y . Finally, we observe that in fully developed NW ensembles, the substrate no longer influences growth kinetics and the same N-limited axial growth rate is measured on both substrates. We conclude that the same nucleation and growth processes take place on a-Al x O y as on nitridated Si and that these processes are of a general nature. Quantitatively, nucleation proceeds somewhat differently, which indicates the influence of the substrate, but once shadowing limits growth processes to the upper part of the NW ensemble, they are not affected anymore by the type of substrate.
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Self-stabilized narrow-bandwidth and high-fidelity entangled photons generated from cold atoms
NASA Astrophysics Data System (ADS)
Yu, Y. C.; Ding, D. S.; Dong, M. X.; Shi, S.; Zhang, W.; Shi, B. S.
2018-04-01
Entangled photon pairs are critically important in fundamental quantum mechanics research as well as in many areas within the field of quantum information, such as quantum communication, quantum computation, and quantum cryptography. Previous demonstrations of entangled photons based on atomic ensembles were achieved by using a reference laser to stabilize the phase of two spontaneous four-wave mixing paths. Here, we demonstrate a convenient and efficient scheme to generate polarization-entangled photons with a narrow bandwidth of 57.2 ±1.6 MHz and a high-fidelity of 96.3 ±0.8 % by using a phase self-stabilized multiplexing system formed by two beam displacers and two half-wave plates where the relative phase between the different signal paths can be eliminated completely. It is possible to stabilize an entangled photon pair for a long time with this system and produce all four Bell states, making this a vital step forward in the field of quantum information.
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Sequence Based Prediction of Antioxidant Proteins Using a Classifier Selection Strategy
Zhang, Lina; Zhang, Chengjin; Gao, Rui; Yang, Runtao; Song, Qing
2016-01-01
Antioxidant proteins perform significant functions in maintaining oxidation/antioxidation balance and have potential therapies for some diseases. Accurate identification of antioxidant proteins could contribute to revealing physiological processes of oxidation/antioxidation balance and developing novel antioxidation-based drugs. In this study, an ensemble method is presented to predict antioxidant proteins with hybrid features, incorporating SSI (Secondary Structure Information), PSSM (Position Specific Scoring Matrix), RSA (Relative Solvent Accessibility), and CTD (Composition, Transition, Distribution). The prediction results of the ensemble predictor are determined by an average of prediction results of multiple base classifiers. Based on a classifier selection strategy, we obtain an optimal ensemble classifier composed of RF (Random Forest), SMO (Sequential Minimal Optimization), NNA (Nearest Neighbor Algorithm), and J48 with an accuracy of 0.925. A Relief combined with IFS (Incremental Feature Selection) method is adopted to obtain optimal features from hybrid features. With the optimal features, the ensemble method achieves improved performance with a sensitivity of 0.95, a specificity of 0.93, an accuracy of 0.94, and an MCC (Matthew’s Correlation Coefficient) of 0.880, far better than the existing method. To evaluate the prediction performance objectively, the proposed method is compared with existing methods on the same independent testing dataset. Encouragingly, our method performs better than previous studies. In addition, our method achieves more balanced performance with a sensitivity of 0.878 and a specificity of 0.860. These results suggest that the proposed ensemble method can be a potential candidate for antioxidant protein prediction. For public access, we develop a user-friendly web server for antioxidant protein identification that is freely accessible at http://antioxidant.weka.cc. PMID:27662651
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Efficient collective influence maximization in cascading processes with first-order transitions
Pei, Sen; Teng, Xian; Shaman, Jeffrey; Morone, Flaviano; Makse, Hernán A.
2017-01-01
In many social and biological networks, the collective dynamics of the entire system can be shaped by a small set of influential units through a global cascading process, manifested by an abrupt first-order transition in dynamical behaviors. Despite its importance in applications, efficient identification of multiple influential spreaders in cascading processes still remains a challenging task for large-scale networks. Here we address this issue by exploring the collective influence in general threshold models of cascading process. Our analysis reveals that the importance of spreaders is fixed by the subcritical paths along which cascades propagate: the number of subcritical paths attached to each spreader determines its contribution to global cascades. The concept of subcritical path allows us to introduce a scalable algorithm for massively large-scale networks. Results in both synthetic random graphs and real networks show that the proposed method can achieve larger collective influence given the same number of seeds compared with other scalable heuristic approaches. PMID:28349988
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Efficient collective influence maximization in cascading processes with first-order transitions
NASA Astrophysics Data System (ADS)
Pei, Sen; Teng, Xian; Shaman, Jeffrey; Morone, Flaviano; Makse, Hernán A.
2017-03-01
In many social and biological networks, the collective dynamics of the entire system can be shaped by a small set of influential units through a global cascading process, manifested by an abrupt first-order transition in dynamical behaviors. Despite its importance in applications, efficient identification of multiple influential spreaders in cascading processes still remains a challenging task for large-scale networks. Here we address this issue by exploring the collective influence in general threshold models of cascading process. Our analysis reveals that the importance of spreaders is fixed by the subcritical paths along which cascades propagate: the number of subcritical paths attached to each spreader determines its contribution to global cascades. The concept of subcritical path allows us to introduce a scalable algorithm for massively large-scale networks. Results in both synthetic random graphs and real networks show that the proposed method can achieve larger collective influence given the same number of seeds compared with other scalable heuristic approaches.
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Park, Wooram; Liu, Yan; Zhou, Yu; Moses, Matthew; Chirikjian, Gregory S
2008-04-11
A nonholonomic system subjected to external noise from the environment, or internal noise in its own actuators, will evolve in a stochastic manner described by an ensemble of trajectories. This ensemble of trajectories is equivalent to the solution of a Fokker-Planck equation that typically evolves on a Lie group. If the most likely state of such a system is to be estimated, and plans for subsequent motions from the current state are to be made so as to move the system to a desired state with high probability, then modeling how the probability density of the system evolves is critical. Methods for solving Fokker-Planck equations that evolve on Lie groups then become important. Such equations can be solved using the operational properties of group Fourier transforms in which irreducible unitary representation (IUR) matrices play a critical role. Therefore, we develop a simple approach for the numerical approximation of all the IUR matrices for two of the groups of most interest in robotics: the rotation group in three-dimensional space, SO(3), and the Euclidean motion group of the plane, SE(2). This approach uses the exponential mapping from the Lie algebras of these groups, and takes advantage of the sparse nature of the Lie algebra representation matrices. Other techniques for density estimation on groups are also explored. The computed densities are applied in the context of probabilistic path planning for kinematic cart in the plane and flexible needle steering in three-dimensional space. In these examples the injection of artificial noise into the computational models (rather than noise in the actual physical systems) serves as a tool to search the configuration spaces and plan paths. Finally, we illustrate how density estimation problems arise in the characterization of physical noise in orientational sensors such as gyroscopes.
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Unlabored system motion by specially conditioned electromagnetic fields in higher dimensional realms
NASA Astrophysics Data System (ADS)
David Froning, H.; Meholic, Gregory V.
2010-01-01
This third of three papers explores the possibility of swift, stress-less system transitions between slower-than-light and faster-than-light speeds with negligible net expenditure of system energetics. The previous papers derived a realm of higher dimensionality than 4-D spacetime that enabled such unlabored motion; and showed that fields that could propel and guide systems on unlabored paths in the higher dimensional realm must be fields that have been conditioned to SU(2) (or higher) Lie group symmetry. This paper shows that the system's surrounding vacuum dielectric ɛμ, within the higher dimensional realm's is a vector (not scalar) quantity with fixed magnitude ɛ0μ0 and changing direction within the realm with changing system speed. Thus, ɛμ generated by the system's EM field must remain tuned to vacuum ɛ0μ0 in both magnitude and direction during swift, unlabored system transitions between slower and faster than light speeds. As a result, the system's changing path and speed is such that the magnitude of the higher dimensional realm's ɛ0μ0 is not disturbed. And it is shown that a system's flight trajectories associated with its swift, unlabored transitions between zero and infinite speed can be represented by curved paths traced-out within the higher dimensional realm.
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NASA Astrophysics Data System (ADS)
Zhao, Liang; Xu, Shun; Tu, Yu-Song; Zhou, Xin
2017-06-01
Not Available Project supported by the National Natural Science Foundation for Outstanding Young Scholars, China (Grant No. 11422542), the National Natural Science Foundation of China (Grant Nos. 11605151 and 11675138), and the Shanghai Supercomputer Center of China and Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase).
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Characterization of Mesoscale Predictability
2013-09-30
2009), which, it had been argued, had high mesoscale predictability. More recently, we have considered the prediction of lowland snow in the Puget ...averaged total and perturbation kinetic energy spectra on the 5-km, convection-permitting grid. The ensembles clearly captured the observed k-5/3 total...kinetic energy spectrum at wavelengths less than approximately 400 km and also showed a transition to a roughly k-3 dependence at longer wavelengths
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The Senior Year: Culminating Experiences and Transitions
ERIC Educational Resources Information Center
Hunter, Mary Stuart, Ed.; Keup, Jennifer R., Ed.; Kinzie, Jillian, Ed.; Maietta, Heather, Ed.
2012-01-01
Increasing pressures on colleges and universities to ensure degree completion and job placement as measures of success make it imperative that the path to graduation is clear and that seniors receive the support needed to earn a degree and make a successful transition to life beyond college. This new edited collection describes today's college…
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Attachment, Well-Being, and College Senior Concerns about the Transition out of College
ERIC Educational Resources Information Center
Lane, Joel A.
2016-01-01
This study examined the relationships among attachment, psychological well-being (PWB), life satisfaction, and concerns about the transition out of college among a sample of college seniors. A path analysis was conducted predicting that PWB and life satisfaction would mediate the relationships between attachment and 3 types of graduation…
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Youth Transition to Employment in Vietnam: A Vulnerable Path
ERIC Educational Resources Information Center
Tran, Thi Tuyet
2018-01-01
Literature suggests that educational attainment is one of the significant factors affecting youth transition to work. The process of capital accumulation through education is suggested as the key marker of social inclusion and exclusion. This paper compares the educational attainment among youth in Vietnam with their status in employment. It uses…
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Technologies and Species Transitions: Polanyi, on a Path to Posthumanity?
ERIC Educational Resources Information Center
Doede, Robert
2011-01-01
Polanyi and Transhumanism both place technologies in pivotal roles in bringing about "Homo sapiens"' species transitions. The question is asked whether Polanyi's emphasis on the role of technology in "Homo sapiens"' rise out of mute beasthood indicates that he might have been inclined to embrace the Transhumanist vision of "Homo sapiens"'…
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ERIC Educational Resources Information Center
Wang, Yan; Ye, Feifei; Pilarzyk, Tom
2014-01-01
This study used a strategic enrollment management (SEM) approach to studying high school students' transition to a two-year college and their initial college success. Path analyses suggested two important findings: (a) clear career choices among students, family influence, academic preparedness, and college recruitment efforts predicted earlier…
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Multiple-Quantum Transitions and Charge-Induced Decoherence of Donor Nuclear Spins in Silicon
NASA Astrophysics Data System (ADS)
Franke, David P.; Pflüger, Moritz P. D.; Itoh, Kohei M.; Brandt, Martin S.
2017-06-01
We study single- and multiquantum transitions of the nuclear spins of an ensemble of ionized arsenic donors in silicon and find quadrupolar effects on the coherence times, which we link to fluctuating electrical field gradients present after the application of light and bias voltage pulses. To determine the coherence times of superpositions of all orders in the 4-dimensional Hilbert space, we use a phase-cycling technique and find that, when electrical effects were allowed to decay, these times scale as expected for a fieldlike decoherence mechanism such as the interaction with surrounding
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Longevial, Jean-François; Clément, Sébastien; Wytko, Jennifer A; Ruppert, Romain; Weiss, Jean; Richeter, Sébastien
2018-04-24
Porphyrins are conjugated, stable chromophores with a central core that binds a variety of metal ions and an easily functionalized peripheral framework. By combining the catalytic, electronic or cytotoxic properties of selected transition metal complexes with the binding and electronic properties of porphyrins, enhanced characteristics of the ensemble are generated. This review article focuses on porphyrins bearing one or more peripheral transition metal complexes and discusses their potential applications in catalysis or biomedicine. Modulation of the electronic properties and intramolecular communication through coordination bond linkages in bis-porphyrin scaffolds is also presented. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Effects of the interaction range on structural phases of flexible polymers.
Gross, J; Neuhaus, T; Vogel, T; Bachmann, M
2013-02-21
We systematically investigate how the range of interaction between non-bonded monomers influences the formation of structural phases of elastic, flexible polymers. Massively parallel replica-exchange simulations of a generic, coarse-grained model, performed partly on graphics processing units and in multiple-gaussian modified ensembles, pave the way for the construction of the structural phase diagram, parametrized by interaction range and temperature. Conformational transitions between gas-like, liquid, and diverse solid (pseudo) phases are identified by microcanonical statistical inflection-point analysis. We find evidence for finite-size effects that cause the crossover of "collapse" and "freezing" transitions for very short interaction ranges.
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Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.
Banerjee, Rahul; Cukier, Robert I
2014-03-20
Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformers. In the MD trajectory, only four of the eight backbone dihedrals exhibit bistable behavior. Defining a conformer as the string XXXX with X = "+" or "-" denoting, respectively, positive or negative values of a given dihedral angle and obtaining the populations of these conformers shows that only four conformers are highly populated, implying a strong correlation among these dihedrals. Clustering in dihedral space to construct the MSM finds the same four bistable dihedral angles. These state populations are very similar to those found directly from the MD trajectory. TPT is used to obtain pathways, parametrized by committor values, in dihedral state space that are followed in transitioning from closed to open states. Pathway costs are estimated by introducing a kinetics-based procedure that orders pathways from least (shortest) to greater cost paths. The least costly pathways in dihedral space are found to only involve the same XXXX set of dihedral angles, and the conformers accessed in the closed to open transition pathways are identified. For these major pathways, a correlation between reaction path progress (committors) and the end-to-end distance is identified. A dihedral space principal component analysis of the MD trajectory shows that the first three modes capture most of the overall fluctuation, and pick out the same four dihedrals having essentially all the weight in those modes. A MSM based on root-mean-square backbone clustering was also carried out, with good agreement found with dihedral clustering for the static information, but with results that differ significantly for the pathway analysis.
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Becky K. Kerns; Ayn J. Shlisky; Colin J. Daniel
2012-01-01
The first ever Landscape State-and-Transition Simulation Modeling Conference was held from June 14â16, 2011, in Portland Oregon. The conference brought together over 70 users of state-and-transition simulation modeling toolsâthe Vegetation Dynamics Development Tool (VDDT), the Tool for Exploratory Landscape Analysis (TELSA) and the Path Landscape Model. The goal of the...
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Giovambattista, Nicolas; Sciortino, Francesco; Starr, Francis W; Poole, Peter H
2016-12-14
The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics to describe supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that low-density liquid (LDL) configurations are located in the same megabasin as LDA, and that high-density liquid (HDL) configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid is different from the path followed by the amorphous solid. At higher pressure, we also study the liquid-to-ice-VII first-order phase transition, and find that the behavior of the PEL properties across this transition is qualitatively similar to the changes found during the LDA-HDA transformation. This similarity supports the interpretation that the LDA-HDA transformation is a first-order phase transition between out-of-equilibrium states. Finally, we compare the PEL properties explored during the LDA-HDA transformations in ST2 water with those reported previously for SPC/E water, for which the LDA-HDA transformations are rather smooth. This comparison illuminates the previous work showing that, at accessible computer times scales, a liquid-liquid phase transition occurs in the case of ST2 water, but not for SPC/E water.
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NASA Astrophysics Data System (ADS)
Giovambattista, Nicolas; Sciortino, Francesco; Starr, Francis W.; Poole, Peter H.
2016-12-01
The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics to describe supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that low-density liquid (LDL) configurations are located in the same megabasin as LDA, and that high-density liquid (HDL) configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid is different from the path followed by the amorphous solid. At higher pressure, we also study the liquid-to-ice-VII first-order phase transition, and find that the behavior of the PEL properties across this transition is qualitatively similar to the changes found during the LDA-HDA transformation. This similarity supports the interpretation that the LDA-HDA transformation is a first-order phase transition between out-of-equilibrium states. Finally, we compare the PEL properties explored during the LDA-HDA transformations in ST2 water with those reported previously for SPC/E water, for which the LDA-HDA transformations are rather smooth. This comparison illuminates the previous work showing that, at accessible computer times scales, a liquid-liquid phase transition occurs in the case of ST2 water, but not for SPC/E water.
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Direct observation of molecular cooperativity near the glass transition.
Russell, E V; Israeloff, N E
2000-12-07
The increasingly sluggish response of a supercooled liquid as it nears its glass transition (for example, refrigerated honey) is prototypical of glassy dynamics found in proteins, neural networks and superconductors. The notion that molecules rearrange cooperatively has long been postulated to explain diverging relaxation times and broadened (non-exponential) response functions near the glass transition. Recently, cooperativity was observed and analysed in colloid glasses and in simulations of binary liquids well above the glass transition. But nanometre-scale studies of cooperativity at the molecular glass transition are lacking. Important issues to be resolved include the precise form of the cooperativity and its length scale, and whether the broadened response is intrinsic to individual cooperative regions, or arises only from heterogeneity in an ensemble of such regions. Here we describe direct observations of molecular cooperativity near the glass transition in polyvinylacetate (PVAc), using nanometre-scale probing of dielectric fluctuations. Molecular clusters switched spontaneously among two to four distinct configurations, producing random telegraph noise. Our analysis of these noise signals and their power spectra reveals that individual clusters exhibit transient dynamical heterogeneity and non-exponential kinetics.
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Semantic labeling of high-resolution aerial images using an ensemble of fully convolutional networks
NASA Astrophysics Data System (ADS)
Sun, Xiaofeng; Shen, Shuhan; Lin, Xiangguo; Hu, Zhanyi
2017-10-01
High-resolution remote sensing data classification has been a challenging and promising research topic in the community of remote sensing. In recent years, with the rapid advances of deep learning, remarkable progress has been made in this field, which facilitates a transition from hand-crafted features designing to an automatic end-to-end learning. A deep fully convolutional networks (FCNs) based ensemble learning method is proposed to label the high-resolution aerial images. To fully tap the potentials of FCNs, both the Visual Geometry Group network and a deeper residual network, ResNet, are employed. Furthermore, to enlarge training samples with diversity and gain better generalization, in addition to the commonly used data augmentation methods (e.g., rotation, multiscale, and aspect ratio) in the literature, aerial images from other datasets are also collected for cross-scene learning. Finally, we combine these learned models to form an effective FCN ensemble and refine the results using a fully connected conditional random field graph model. Experiments on the ISPRS 2-D Semantic Labeling Contest dataset show that our proposed end-to-end classification method achieves an overall accuracy of 90.7%, a state-of-the-art in the field.
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Hyper-Parallel Tempering Monte Carlo Method and It's Applications
NASA Astrophysics Data System (ADS)
Yan, Qiliang; de Pablo, Juan
2000-03-01
A new generalized hyper-parallel tempering Monte Carlo molecular simulation method is presented for study of complex fluids. The method is particularly useful for simulation of many-molecule complex systems, where rough energy landscapes and inherently long characteristic relaxation times can pose formidable obstacles to effective sampling of relevant regions of configuration space. The method combines several key elements from expanded ensemble formalisms, parallel-tempering, open ensemble simulations, configurational bias techniques, and histogram reweighting analysis of results. It is found to accelerate significantly the diffusion of a complex system through phase-space. In this presentation, we demonstrate the effectiveness of the new method by implementing it in grand canonical ensembles for a Lennard-Jones fluid, for the restricted primitive model of electrolyte solutions (RPM), and for polymer solutions and blends. Our results indicate that the new algorithm is capable of overcoming the large free energy barriers associated with phase transitions, thereby greatly facilitating the simulation of coexistence properties. It is also shown that the method can be orders of magnitude more efficient than previously available techniques. More importantly, the method is relatively simple and can be incorporated into existing simulation codes with minor efforts.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Shi, Jade; Nobrega, R. Paul; Schwantes, Christian
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structuremore » of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.« less
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Near-Unity Internal Quantum Efficiency of Luminescent Silicon Nanocrystals with Ligand Passivation.
Sangghaleh, Fatemeh; Sychugov, Ilya; Yang, Zhenyu; Veinot, Jonathan G C; Linnros, Jan
2015-07-28
Spectrally resolved photoluminescence (PL) decays were measured for samples of colloidal, ligand-passivated silicon nanocrystals. These samples have PL emission energies with peak positions in the range ∼1.4-1.8 eV and quantum yields of ∼30-70%. Their ensemble PL decays are characterized by a stretched-exponential decay with a dispersion factor of ∼0.8, which changes to an almost monoexponential character at fixed detection energies. The dispersion factors and decay rates for various detection energies were extracted from spectrally resolved curves using a mathematical approach that excluded the effect of homogeneous line width broadening. Since nonradiative recombination would introduce a random lifetime variation, leading to a stretched-exponential decay for an ensemble, we conclude that the observed monoexponential decay in size-selected ensembles signifies negligible nonradiative transitions of a similar strength to the radiative one. This conjecture is further supported as extracted decay rates agree with radiative rates reported in the literature, suggesting 100% internal quantum efficiency over a broad range of emission wavelengths. The apparent differences in the quantum yields can then be explained by a varying fraction of "dark" or blinking nanocrystals.
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Exact transition probabilities in a 6-state Landau–Zener system with path interference
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sinitsyn, Nikolai A.
2015-04-23
In this paper, we identify a nontrivial multistate Landau–Zener (LZ) model for which transition probabilities between any pair of diabatic states can be determined analytically and exactly. In the semiclassical picture, this model features the possibility of interference of different trajectories that connect the same initial and final states. Hence, transition probabilities are generally not described by the incoherent successive application of the LZ formula. Finally, we discuss reasons for integrability of this system and provide numerical tests of the suggested expression for the transition probability matrix.
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Constrained proper sampling of conformations of transition state ensemble of protein folding
Lin, Ming; Zhang, Jian; Lu, Hsiao-Mei; Chen, Rong; Liang, Jie
2011-01-01
Characterizing the conformations of protein in the transition state ensemble (TSE) is important for studying protein folding. A promising approach pioneered by Vendruscolo [Nature (London) 409, 641 (2001)] to study TSE is to generate conformations that satisfy all constraints imposed by the experimentally measured ϕ values that provide information about the native likeness of the transition states. Faísca [J. Chem. Phys. 129, 095108 (2008)] generated conformations of TSE based on the criterion that, starting from a TS conformation, the probabilities of folding and unfolding are about equal through Markov Chain Monte Carlo (MCMC) simulations. In this study, we use the technique of constrained sequential Monte Carlo method [Lin , J. Chem. Phys. 129, 094101 (2008); Zhang Proteins 66, 61 (2007)] to generate TSE conformations of acylphosphatase of 98 residues that satisfy the ϕ-value constraints, as well as the criterion that each conformation has a folding probability of 0.5 by Monte Carlo simulations. We adopt a two stage process and first generate 5000 contact maps satisfying the ϕ-value constraints. Each contact map is then used to generate 1000 properly weighted conformations. After clustering similar conformations, we obtain a set of properly weighted samples of 4185 candidate clusters. Representative conformation of each of these cluster is then selected and 50 runs of Markov chain Monte Carlo (MCMC) simulation are carried using a regrowth move set. We then select a subset of 1501 conformations that have equal probabilities to fold and to unfold as the set of TSE. These 1501 samples characterize well the distribution of transition state ensemble conformations of acylphosphatase. Compared with previous studies, our approach can access much wider conformational space and can objectively generate conformations that satisfy the ϕ-value constraints and the criterion of 0.5 folding probability without bias. In contrast to previous studies, our results show that transition state conformations are very diverse and are far from nativelike when measured in cartesian root-mean-square deviation (cRMSD): the average cRMSD between TSE conformations and the native structure is 9.4 Å for this short protein, instead of 6 Å reported in previous studies. In addition, we found that the average fraction of native contacts in the TSE is 0.37, with enrichment in native-like β-sheets and a shortage of long range contacts, suggesting such contacts form at a later stage of folding. We further calculate the first passage time of folding of TSE conformations through calculation of physical time associated with the regrowth moves in MCMC simulation through mapping such moves to a Markovian state model, whose transition time was obtained by Langevin dynamics simulations. Our results indicate that despite the large structural diversity of the TSE, they are characterized by similar folding time. Our approach is general and can be used to study TSE in other macromolecules. PMID:21341875
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Spring operated accelerator and constant force spring mechanism therefor
NASA Technical Reports Server (NTRS)
Shillinger, G. L., Jr. (Inventor)
1977-01-01
A spring assembly consisting of an elongate piece of flat spring material formed into a spiral configuration and a free running spool in circumscribing relation to which this spring is disposed was developed. The spring has a distal end that is externally accessible so that when the distal end is drawn along a path, the spring unwinds against a restoring force present in the portion of the spring that resides in a transition region between a relatively straight condition on the path and a fully wound condition on the spool. When the distal end is released, the distal end is accelerated toward the spool by the force existing at the transition region which force is proportional to the cross-sectional area of the spring.
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Study of the De-Icing Properties of the ASDE-3 Rotodome.
1982-04-01
Heat Transfer Coefficients ........................... 3 -18 3.2.3 Prediction of De-Icing Capability ...... 3 -23 3.2.4 Calculation of Mean DIA & PATH...kVA 3 -31 N NUL =ti: :6 i ::p :: %:::::28 -R) [ eN 23,100t Averaged for Laminar & Turbulent Regimes. SAssuming a transition from Laminar to. Turbulent...Calculation of Mean Dia .& Path Length for Roof Mean Path Length for Roof: y 4r 4x 9 3.82 ft 3 x 7 1 2(92 3.8221/2 1 = 2(92 - 3.822 = 8.15 ft x 2 16.3 ft 16.3
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NASA Astrophysics Data System (ADS)
Hayata, Tomoya; Hidaka, Yoshimasa; Noumi, Toshifumi; Hongo, Masaru
2015-09-01
We derive relativistic hydrodynamics from quantum field theories by assuming that the density operator is given by a local Gibbs distribution at initial time. We decompose the energy-momentum tensor and particle current into nondissipative and dissipative parts, and analyze their time evolution in detail. Performing the path-integral formulation of the local Gibbs distribution, we microscopically derive the generating functional for the nondissipative hydrodynamics. We also construct a basis to study dissipative corrections. In particular, we derive the first-order dissipative hydrodynamic equations without a choice of frame such as the Landau-Lifshitz or Eckart frame.
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Coherent transmission of an ultrasonic shock wave through a multiple scattering medium.
Viard, Nicolas; Giammarinaro, Bruno; Derode, Arnaud; Barrière, Christophe
2013-08-01
We report measurements of the transmitted coherent (ensemble-averaged) wave resulting from the interaction of an ultrasonic shock wave with a two-dimensional random medium. Despite multiple scattering, the coherent waveform clearly shows the steepening that is typical of nonlinear harmonic generation. This is taken advantage of to measure the elastic mean free path and group velocity over a broad frequency range (2-15 MHz) in only one experiment. Experimental results are found to be in good agreement with a linear theoretical model taking into account spatial correlations between scatterers. These results show that nonlinearity and multiple scattering are both present, yet uncoupled.
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Diffusion of strongly magnetized cosmic ray particles in a turbulent medium
NASA Technical Reports Server (NTRS)
Ptuskin, V. S.
1985-01-01
Cosmic ray (CR) propagation in a turbulent medium is usually considered in the diffusion approximation. Here, the diffusion equation is obtained for strongly magnetized particles in the general form. The influence of a large-scale random magnetic field on CR propagation in interstellar medium is discussed. Cosmic rays are assumed to propagate in a medium with a regular field H and an ensemble of random MHD waves. The energy density of waves on scales smaller than the free path 1 of CR particles is small. The collision integral of the general form which describes interaction between relativistic particles and waves in the quasilinear approximation is used.
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Path integrals, the ABL rule and the three-box paradox
NASA Astrophysics Data System (ADS)
Sokolovski, D.; Puerto Giménez, I.; Sala Mayato, R.
2008-10-01
The three-box problem is analysed in terms of virtual pathways, interference between which is destroyed by a number of intermediate measurements. The Aharonov-Bergmann-Lebowitz (ABL) rule is shown to be a particular case of Feynman's recipe for assigning probabilities to exclusive alternatives. The ‘paradoxical’ features of the three box case arise in an attempt to attribute, in contradiction to the uncertainty principle, properties pertaining to different ensembles produced by different intermediate measurements to the same particle. The effect can be mimicked by a classical system, provided an observation is made to perturb the system in a non-local manner.
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It's My Life! Career Paths for Young Women in Transition. Coordinator's Handbook.
ERIC Educational Resources Information Center
Florio, Carol; And Others
This document is the coordinator's handbook for a four-day workshop for young women in transition from high school to two-year colleges. The program covers career information, self-awareness and skills assessment (with special regard for mathematics), the many roles of women, and decision making and planning. It includes large- and small-group…
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Suicidal or Self-Harming Ideation in Military Personnel Transitioning to Civilian Life
ERIC Educational Resources Information Center
Mansfield, Alyssa J.; Bender, Randall H.; Hourani, Laurel L.; Larson, Gerald E.
2011-01-01
Suicides have markedly increased among military personnel in recent years. We used path analysis to examine factors associated with suicidal/self-harming ideation among male Navy and Marine Corps personnel transitioning to civilian life. Roughly 7% of men (Sailors = 5.3%, Marines = 9.0%) reported ideation during the previous 30 days. Results…
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Becky K. Kerns; Miles A. Hemstrom; David Conklin; Gabriel I. Yospin; Bart Johnson; Dominique Bachelet; Scott Bridgham
2012-01-01
Understanding landscape vegetation dynamics often involves the use of scientifically-based modeling tools that are capable of testing alternative management scenarios given complex ecological, management, and social conditions. State-and-transition simulation model (STSM) frameworks and software such as PATH and VDDT are commonly used tools that simulate how landscapes...
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Lost in Transition: Building a Better Path from School to College and Careers
ERIC Educational Resources Information Center
Bottoms, Gene; Young, Marna
2008-01-01
In 2005 and 2006, the "High Schools That Work" ("HSTW") program of the Southern Regional Education Board (SREB) and the College and Career Transitions Initiative of the League for Innovation in the Community College (League) facilitated a series of 15 state-level forums aimed at identifying ways to foster collaboration between secondary and…
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Architecting Technology Transition Pathways: Insights from the Military Tactical Network Upgrade
2015-05-08
effective transition path design...1. Introduction Today’s engineering systems are increasingly complex and interdependent. As part of this trend, the luxury of green‐field design...operations can’t take effect until all or most of the airframes have the new equipment. Since the cost‐burden will be unequally born by airlines
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Is History Destiny? Resources, Transitions and Child Education Attainments in Canada. Final Report
ERIC Educational Resources Information Center
Hoddinott, John; Lethbridge, Lynn; Phipps, Shelley
2002-01-01
This paper examines three inter-related issues: whether past levels of resources, context and opportunity structures carry long-term consequences for subsequent child attainments and behaviours; whether shocks, or transition events, alter the path of these outcomes in a positive or negative fashion; and what role can be played by policy…
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Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol
2015-01-01
Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled. PMID:25516726
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Theory of Disk-to-Vesicle Transformation
NASA Astrophysics Data System (ADS)
Li, Jianfeng; Shi, An-Chang
2009-03-01
Self-assembled membranes from amphiphilic molecules, such as lipids and block copolymers, can assume a variety of morphologies dictated by energy minimization of system. The membrane energy is characterized by a bending modulus (κ), a Gaussian modulus (κG), and the line tension (γ) of the edge. Two basic morphologies of membranes are flat disks that minimize the bending energy at the cost of the edge energy, and enclosed vesicles that minimize the edge energy at the cost of bending energy. In our work, the transition from disk to vesicle is studied theoretically using the string method, which is designed to find the minimum energy path (MEP) or the most probable transition path between two local minima of an energy landscape. Previous studies of disk-to-vesicle transition usually approximate the transitional states by a series of spherical cups, and found that the spherical cups do not correspond to stable or meta-stable states of the system. Our calculation demonstrates that the intermediate shapes along the MEP are very different from spherical cups. Furthermore, some of these transitional states can be meta-stable. The disk-to-vesicle transition pathways are governed by two scaled parameters, κG/κ and γR0/4κ, where R0 is the radius of the disk. In particular, a meta-stable intermediate state is predicted, which may correspond to the open morphologies observed in experiments and simulations.
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Sesé, Luis M; Bailey, Lorna E
2007-04-28
The structural features of the quantum hard-sphere system in the region of the fluid-face-centered-cubic-solid transition, for reduced number densities 0.45
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Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins
NASA Astrophysics Data System (ADS)
Seyler, Sean L.
In a typical living cell, millions to billions of proteins--nanomachines that fluctuate and cycle among many conformational states--convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible. Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)--an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project--developing a hybrid atomistic-continuum method--is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
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Unexpected manifestation of quark condensation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zinovjev, G. M., E-mail: Gennady.Zinovjev@cern.ch; Molodtsov, S. V.
A comparative analysis of some quark ensembles governed by a four-fermion interaction is performed. Arguments in support of the statement that the presence of a gas-liquid phase transition is a feature peculiar to them are adduced. The instability of small quark droplets is discussed and is attributed to the formation of a chiral soliton. The stability of baryon matter is due to a mixed phase of the vacuum and baryon matter.
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2010-06-01
Demonstration of an area-enclosing guided-atom interferometer for rotation sensing, Phys. Rev. Lett. 99, 173201 (2007). 4. Heralded Single- Magnon Quantum...excitations are quantized spin waves ( magnons ), such that transitions between its energy levels ( magnon number states) correspond to highly directional...polarization storage in the form of a single collective-spin excitation ( magnon ) that is shared between two spatially overlapped atomic ensembles
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Structural dynamics of free proteins in diffraction.
Lin, Milo M; Shorokhov, Dmitry; Zewail, Ahmed H
2011-10-26
Among the macromolecular patterns of biological significance, right-handed α-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix-coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an α-helical protein segment thymosin β(9) (Tβ(9)), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix-coil transitions in Tβ(9), in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (α-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly, the decay of α-helical motifs and the (globular) conformational annealing in Tβ(9) occur consecutively or competitively, depending on the magnitude of temperature jump.
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NASA Astrophysics Data System (ADS)
Orkoulas, Gerassimos; Panagiotopoulos, Athanassios Z.
1994-07-01
In this work, we investigate the liquid-vapor phase transition of the restricted primitive model of ionic fluids. We show that at the low temperatures where the phase transition occurs, the system cannot be studied by conventional molecular simulation methods because convergence to equilibrium is slow. To accelerate convergence, we propose cluster Monte Carlo moves capable of moving more than one particle at a time. We then address the issue of charged particle transfers in grand canonical and Gibbs ensemble Monte Carlo simulations, for which we propose a biased particle insertion/destruction scheme capable of sampling short interparticle distances. We compute the chemical potential for the restricted primitive model as a function of temperature and density from grand canonical Monte Carlo simulations and the phase envelope from Gibbs Monte Carlo simulations. Our calculated phase coexistence curve is in agreement with recent results of Caillol obtained on the four-dimensional hypersphere and our own earlier Gibbs ensemble simulations with single-ion transfers, with the exception of the critical temperature, which is lower in the current calculations. Our best estimates for the critical parameters are T*c=0.053, ρ*c=0.025. We conclude with possible future applications of the biased techniques developed here for phase equilibrium calculations for ionic fluids.
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An experimental investigation of gas fuel injection with X-ray radiography
Swantek, Andrew B.; Duke, D. J.; Kastengren, A. L.; ...
2017-04-21
In this paper, an outward-opening compressed natural gas, direct injection fuel injector has been studied with single-shot x-ray radiography. Three dimensional simulations have also been performed to compliment the x-ray data. Argon was used as a surrogate gas for experimental and safety reasons. This technique allows the acquisition of a quantitative mapping of the ensemble-average and standard deviation of the projected density throughout the injection event. Two dimensional, ensemble average and standard deviation data are presented to investigate the quasi-steady-state behavior of the jet. Upstream of the stagnation zone, minimal shot-to-shot variation is observed. Downstream of the stagnation zone, bulkmore » mixing is observed as the jet transitions to a subsonic turbulent jet. From the time averaged data, individual slices at all downstream locations are extracted and an Abel inversion was performed to compute the radial density distribution, which was interpolated to create three dimensional visualizations. The Abel reconstructions reveal that upstream of the stagnation zone, the gas forms an annulus with high argon density and large density gradients. Inside this annulus, a recirculation region with low argon density exists. Downstream, the jet transitions to a fully turbulent jet with Gaussian argon density distributions. This experimental data is intended to serve as a quantitative benchmark for simulations.« less
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Solid-state ensemble of highly entangled photon sources at rubidium atomic transitions
NASA Astrophysics Data System (ADS)
Zopf, Michael; Keil, Robert; Chen, Yan; HöFer, Bianca; Zhang, Jiaxiang; Ding, Fei; Schmidt, Oliver G.
Semiconductor InAs/GaAs quantum dots grown by the Stranski-Krastanov method are among the leading candidates for the deterministic generation of polarization entangled photon pairs. Despite remarkable progress in the last twenty years, many challenges still remain for this material, such as the extremely low yield (< 1% quantum dots can emit entangled photons), the low degree of entanglement, and the large wavelength distribution. Here we show that, with an emerging family of GaAs/AlGaAs quantum dots grown by droplet etching and nanohole infilling, it is possible to obtain a large ensemble (close to 100%) of polarization-entangled photon emitters on a wafer without any post-growth tuning. Under pulsed resonant two-photon excitation, all measured quantum dots emit single pairs of entangled photons with ultra-high purity, high degree of entanglement (fidelity up to F=0.91, with a record high concurrence C=0.90), and ultra-narrow wavelength distribution at rubidium transitions. Therefore, a solid-state quantum repeater - among many other key enabling quantum photonic elements - can be practically implemented with this new material. Financially supported by BMBF Q.Com-H (16KIS0106) and the Euro- pean Union Seventh Framework Programme 209 (FP7/2007-2013) under Grant Agreement No. 601126 210 (HANAS).
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An experimental investigation of gas fuel injection with X-ray radiography
DOE Office of Scientific and Technical Information (OSTI.GOV)
Swantek, Andrew B.; Duke, D. J.; Kastengren, A. L.
In this paper, an outward-opening compressed natural gas, direct injection fuel injector has been studied with single-shot x-ray radiography. Three dimensional simulations have also been performed to compliment the x-ray data. Argon was used as a surrogate gas for experimental and safety reasons. This technique allows the acquisition of a quantitative mapping of the ensemble-average and standard deviation of the projected density throughout the injection event. Two dimensional, ensemble average and standard deviation data are presented to investigate the quasi-steady-state behavior of the jet. Upstream of the stagnation zone, minimal shot-to-shot variation is observed. Downstream of the stagnation zone, bulkmore » mixing is observed as the jet transitions to a subsonic turbulent jet. From the time averaged data, individual slices at all downstream locations are extracted and an Abel inversion was performed to compute the radial density distribution, which was interpolated to create three dimensional visualizations. The Abel reconstructions reveal that upstream of the stagnation zone, the gas forms an annulus with high argon density and large density gradients. Inside this annulus, a recirculation region with low argon density exists. Downstream, the jet transitions to a fully turbulent jet with Gaussian argon density distributions. This experimental data is intended to serve as a quantitative benchmark for simulations.« less
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Optimization of the transition path of the head hardening with using the genetic algorithms
NASA Astrophysics Data System (ADS)
Wróbel, Joanna; Kulawik, Adam
2016-06-01
An automated method of choice of the transition path of the head hardening in heat treatment process for the plane steel element is proposed in this communication. This method determines the points on the path of moving heat source using the genetic algorithms. The fitness function of the used algorithm is determined on the basis of effective stresses and yield point depending on the phase composition. The path of the hardening tool and also the area of the heat affected zone is determined on the basis of obtained points. A numerical model of thermal phenomena, phase transformations in the solid state and mechanical phenomena for the hardening process is implemented in order to verify the presented method. A finite element method (FEM) was used for solving the heat transfer equation and getting required temperature fields. The moving heat source is modeled with a Gaussian distribution and the water cooling is also included. The macroscopic model based on the analysis of the CCT and CHT diagrams of the medium-carbon steel is used to determine the phase transformations in the solid state. A finite element method is also used for solving the equilibrium equations giving us the stress field. The thermal and structural strains are taken into account in the constitutive relations.
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NASA Astrophysics Data System (ADS)
Resseguier, V.; Memin, E.; Chapron, B.; Fox-Kemper, B.
2017-12-01
In order to better observe and predict geophysical flows, ensemble-based data assimilation methods are of high importance. In such methods, an ensemble of random realizations represents the variety of the simulated flow's likely behaviors. For this purpose, randomness needs to be introduced in a suitable way and physically-based stochastic subgrid parametrizations are promising paths. This talk will propose a new kind of such a parametrization referred to as modeling under location uncertainty. The fluid velocity is decomposed into a resolved large-scale component and an aliased small-scale one. The first component is possibly random but time-correlated whereas the second is white-in-time but spatially-correlated and possibly inhomogeneous and anisotropic. With such a velocity, the material derivative of any - possibly active - tracer is modified. Three new terms appear: a correction of the large-scale advection, a multiplicative noise and a possibly heterogeneous and anisotropic diffusion. This parameterization naturally ensures attractive properties such as energy conservation for each realization. Additionally, this stochastic material derivative and the associated Reynolds' transport theorem offer a systematic method to derive stochastic models. In particular, we will discuss the consequences of the Quasi-Geostrophic assumptions in our framework. Depending on the turbulence amount, different models with different physical behaviors are obtained. Under strong turbulence assumptions, a simplified diagnosis of frontolysis and frontogenesis at the surface of the ocean is possible in this framework. A Surface Quasi-Geostrophic (SQG) model with a weaker noise influence has also been simulated. A single realization better represents small scales than a deterministic SQG model at the same resolution. Moreover, an ensemble accurately predicts extreme events, bifurcations as well as the amplitudes and the positions of the simulation errors. Figure 1 highlights this last result and compares it to the strong error underestimation of an ensemble simulated from the deterministic dynamic with random initial conditions.
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Viruses and mobile elements as drivers of evolutionary transitions.
Koonin, Eugene V
2016-08-19
The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of 'public goods'. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host-parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Authors.
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High-lying single-particle modes, chaos, correlational entropy, and doubling phase transition
DOE Office of Scientific and Technical Information (OSTI.GOV)
Stoyanov, Chavdar; Zelevinsky, Vladimir
Highly excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phononlike modes of the core. In the framework of the quasiparticle-phonon model, we consider the structure of resulting complex configurations, using the 1k{sub 17/2} orbital in {sup 209}Pb as an example. Although, on the level of one- and two-phonon admixtures, the fully chaotic Gaussian orthogonal ensemble regime is not reached, the eigenstates of the model carry a significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the systemmore » undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks. This phase transition is clearly detected by correlational entropy.« less
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Thermodynamics of pairing in mesoscopic systems
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sumaryada, Tony; Volya, Alexander
Using numerical and analytical methods implemented for different models, we conduct a systematic study of the thermodynamic properties of pairing correlations in mesoscopic nuclear systems. Various quantities are calculated and analyzed using the exact solution of pairing. An in-depth comparison of canonical, grand canonical, and microcanonical ensembles is conducted. The nature of the pairing phase transition in a small system is of a particular interest. We discuss the onset of discontinuity in the thermodynamic variables, fluctuations, and evolution of zeros of the canonical and grand canonical partition functions in the complex plane. The behavior of the invariant correlational entropy ismore » also studied in the transitional region of interest. The change in the character of the phase transition due to the presence of a magnetic field is discussed along with studies of superconducting thermodynamics.« less
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Astr 101 Students' Attitudes Towards Essays On Transits, Eclipses And Occultations
NASA Astrophysics Data System (ADS)
D'Cruz, Noella L.
2012-05-01
Joliet Junior College, Joliet, IL offers a one semester introductory astronomy course each semester. We teach over 110 primarily non-science major students each semester. We use proven active learning strategies such lecture tutorials, think-pair-share questions and small group discussions to help these students develop and retain a good understanding of astrophysical concepts. Occasionally, we offer projects that allow students to explore course topics beyond the classroom. We hope that such projects will increase students' interest in astronomy. We also hope that these assignments will help students to improve their critical thinking and writing skills. In Spring 12, we are offering three short individual essay assignments in our face-to-face sections. The essays focus on transits, eclipses and occultations to highlight the 2012 transit of Venus. For the first essay, students will find images of transit and occultation events using the Astronomy Picture of the Day website and describe their chosen events. In addition, students will predict how variations in certain physical and orbital parameters would alter their particular events. The second essay involves transits, eclipses and occultations observed by spacecraft. Students will describe their transit event, their spacecraft's mission, orbital path, how the orbital path was achieved, etc. The third essay deals with transiting exoplanets. Students will choose at least two exoplanets from an exoplanet database, one of which has been discovered through the transit method. This essay will enable students to learn about detecting exoplanets and how they compare with our solar system. Details of the essay assignments and students' reactions to them will be presented at the meeting.
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Temporal dynamics of catchment transit times from stable isotope data
NASA Astrophysics Data System (ADS)
Klaus, Julian; Chun, Kwok P.; McGuire, Kevin J.; McDonnell, Jeffrey J.
2015-06-01
Time variant catchment transit time distributions are fundamental descriptors of catchment function but yet not fully understood, characterized, and modeled. Here we present a new approach for use with standard runoff and tracer data sets that is based on tracking of tracer and age information and time variant catchment mixing. Our new approach is able to deal with nonstationarity of flow paths and catchment mixing, and an irregular shape of the transit time distribution. The approach extracts information on catchment mixing from the stable isotope time series instead of prior assumptions of mixing or the shape of transit time distribution. We first demonstrate proof of concept of the approach with artificial data; the Nash-Sutcliffe efficiencies in tracer and instantaneous transit times were >0.9. The model provides very accurate estimates of time variant transit times when the boundary conditions and fluxes are fully known. We then tested the model with real rainfall-runoff flow and isotope tracer time series from the H.J. Andrews Watershed 10 (WS10) in Oregon. Model efficiencies were 0.37 for the 18O modeling for a 2 year time series; the efficiencies increased to 0.86 for the second year underlying the need of long time tracer time series with a long overlap of tracer input and output. The approach was able to determine time variant transit time of WS10 with field data and showed how it follows the storage dynamics and related changes in flow paths where wet periods with high flows resulted in clearly shorter transit times compared to dry low flow periods.
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NASA Astrophysics Data System (ADS)
Ertaş, Mehmet; Keskin, Mustafa
2015-03-01
By using the path probability method (PPM) with point distribution, we study the dynamic phase transitions (DPTs) in the Blume-Emery-Griffiths (BEG) model under an oscillating external magnetic field. The phases in the model are obtained by solving the dynamic equations for the average order parameters and a disordered phase, ordered phase and four mixed phases are found. We also investigate the thermal behavior of the dynamic order parameters to analyze the nature dynamic transitions as well as to obtain the DPT temperatures. The dynamic phase diagrams are presented in three different planes in which exhibit the dynamic tricritical point, double critical end point, critical end point, quadrupole point, triple point as well as the reentrant behavior, strongly depending on the values of the system parameters. We compare and discuss the dynamic phase diagrams with dynamic phase diagrams that were obtained within the Glauber-type stochastic dynamics based on the mean-field theory.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chen, Hang, E-mail: hangchen@mit.edu; Thill, Peter; Cao, Jianshu
In biochemical systems, intrinsic noise may drive the system switch from one stable state to another. We investigate how kinetic switching between stable states in a bistable network is influenced by dynamic disorder, i.e., fluctuations in the rate coefficients. Using the geometric minimum action method, we first investigate the optimal transition paths and the corresponding minimum actions based on a genetic toggle switch model in which reaction coefficients draw from a discrete probability distribution. For the continuous probability distribution of the rate coefficient, we then consider two models of dynamic disorder in which reaction coefficients undergo different stochastic processes withmore » the same stationary distribution. In one, the kinetic parameters follow a discrete Markov process and in the other they follow continuous Langevin dynamics. We find that regulation of the parameters modulating the dynamic disorder, as has been demonstrated to occur through allosteric control in bistable networks in the immune system, can be crucial in shaping the statistics of optimal transition paths, transition probabilities, and the stationary probability distribution of the network.« less
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Markov State Models of gene regulatory networks.
Chu, Brian K; Tse, Margaret J; Sato, Royce R; Read, Elizabeth L
2017-02-06
Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking. The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models. Application of transition path theory to the constructed Markov State Model decomposes global dynamics into a set of dominant transition paths and associated relative probabilities for stochastic state-switching. In this proof-of-concept study, we found that the Markov State Model provides a general framework for analyzing and visualizing stochastic multistability and state-transitions in gene networks. Our results suggest that this framework-adopted from the field of atomistic Molecular Dynamics-can be a useful tool for quantitative Systems Biology at the network scale.
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Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.
Templeton, Clark; Chen, Szu-Hua; Fathizadeh, Arman; Elber, Ron
2017-10-21
The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system.
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Yu, Tang-Qing; Lapelosa, Mauro; Vanden-Eijnden, Eric; Abrams, Cameron F
2015-03-04
We use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the collective variable space for CO localization in myoglobin to estimate the kinetics of entry, exit, and internal site-hopping. The tessellation is determined by analysis of the free-energy surface in that space using transition-path theory (TPT), which provides criteria for defining optimal milestones, allowing short, independent, cell-constrained MD simulations to provide properly weighted kinetic data. We coarse grain the resulting kinetic model at two levels: first, using crystallographically relevant internal cavities and their predicted interconnections and solvent portals; and second, as a three-state side-path scheme inspired by similar models developed from geminate recombination experiments. We show semiquantitative agreement with experiment on entry and exit rates and in the identification of the so-called "histidine gate" at position 64 through which ≈90% of flux between solvent and the distal pocket passes. We also show with six-dimensional calculations that the minimum free-energy pathway of escape through the histidine gate is a "knock-on" mechanism in which motion of the ligand and the gate are sequential and interdependent. In total, these results suggest that such TPT simulations are indeed a promising approach to overcome the practical time-scale limitations of MD to allow reliable estimation of transition mechanisms and rates among metastable states.
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Complexity in Matuyama-Brunhes polarity transitions from North Atlantic IODP/ODP deep-sea sites
NASA Astrophysics Data System (ADS)
Channell, J. E. T.
2017-06-01
Integrated Ocean Drilling Program (IODP) Expedition 303 to the North Atlantic provided 16 records of the Matuyama-Brunhes polarity transition (MBT), based on u-channel and discrete samples, from holes drilled at three sites (Sites U1304, U1305 and U1306) that have mean Brunhes sedimentation rates of 16-18 cm/kyr. The MBT occurs during the transition from marine isotope stage (MIS) 19c to MIS 18e, with mid-point at ∼773 ka, and a transition duration of ∼8 kyr. Combining the new MBT records, including one new record for the top Jaramillo, with previously published North Atlantic MBT records (ODP Sites 983, 984 and 1063) yields a total of more than 20 high-sedimentation-rate polarity transition records. The MBT yields a repetitive pattern of transitional field states as virtual geomagnetic poles (VGPs) move from high southern latitudes to loop over the Pacific, group in NE Asia, and transit into the mid-latitude South Atlantic before reaching high latitudes in the Northern Hemisphere. The VGPs for the top Jaramillo transition feature a loop over the Pacific, then a NE Asia group before transit over the Indian Ocean to high southerly latitudes. The North Atlantic MBT records described here contrast with longitudinally-constrained VGP paths for the MBT, indicating that relatively low sedimentation rate (∼4 cm/kyr) records of the MBT are heavily smoothed by the remanence acquisition process and do not adequately represent the MBT field. The VGPs at the MBT and top Jaramillo, as measured in the North Atlantic, have similarities with excursion (Iceland Basin) VGP paths, and were apparently guided by maxima in downward vertical flux similar to those seen in the modern non-dipole (ND) field, implying longevity in ND features through time.
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Communication: Adiabatic and non-adiabatic electron-nuclear motion: Quantum and classical dynamics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Albert, Julian; Kaiser, Dustin; Engel, Volker
2016-05-07
Using a model for coupled electronic-nuclear motion we investigate the range from negligible to strong non-adiabatic coupling. In the adiabatic case, the quantum dynamics proceeds in a single electronic state, whereas for strong coupling a complete transition between two adiabatic electronic states takes place. It is shown that in all coupling regimes the short-time wave-packet dynamics can be described using ensembles of classical trajectories in the phase space spanned by electronic and nuclear degrees of freedom. We thus provide an example which documents that the quantum concept of non-adiabatic transitions is not necessarily needed if electronic and nuclear motion ismore » treated on the same footing.« less
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Coherence Measurements for Excited to Excited State Transitions in Barium
NASA Technical Reports Server (NTRS)
Trajmar, S.; Kanik, I.; Karaganov, V.; Zetner, P. W.; Csanak, G.
2000-01-01
Experimental studies concerning elastic and inelastic electron scattering by coherently ensembles of Ba (...6s6p (sub 1)P(sub 1)) atoms with various degrees of alignment will be described. An in-plane, linearly-polarized laser beam was utilized to prepare these target ensembles and the electron scattering signal as a function of polarization angle was measured for several laser geometries at fixed impact energies and scattering angles. From these measurements, we derived cross sections and electron-impact coherence parameters associated with the electron scattering process which is time reverse of the actual experimentally studied process. This interpretation of the experiment is based on the theory of Macek and Herte. The experimental results were also interpreted in terms of cross sections and collision parameters associated with the actual experimental processes. Results obtained so far will be presented and plans for further studies will be discussed.
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Optical vector network analysis of ultranarrow transitions in 166Er3+ : 7LiYF4 crystal.
Kukharchyk, N; Sholokhov, D; Morozov, O; Korableva, S L; Cole, J H; Kalachev, A A; Bushev, P A
2018-02-15
We present optical vector network analysis (OVNA) of an isotopically purified Er166 3+ :LiYF 4 7 crystal. The OVNA method is based on generation and detection of a modulated optical sideband by using a radio-frequency vector network analyzer. This technique is widely used in the field of microwave photonics for the characterization of optical responses of optical devices such as filters and high-Q resonators. However, dense solid-state atomic ensembles induce a large phase shift on one of the optical sidebands that results in the appearance of extra features on the measured transmission response. We present a simple theoretical model that accurately describes the observed spectra and helps to reconstruct the absorption profile of a solid-state atomic ensemble as well as corresponding change of the refractive index in the vicinity of atomic resonances.
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Stimulated emission from ladder-type two-photon coherent atomic ensemble.
Park, Jiho; Moon, Han Seb
2018-05-28
We investigated the stimulated emission from a ladder-type two-photon coherent atomic ensemble, for the 5S 1/2 - 5P 3/2 - 5D 5/2 transition of 87 Rb atoms. Under the ladder-type two-photon resonance condition obtained using pump and coupling lasers, we observed broad four-wave mixing (FWM) light stimulated from two-photon coherence induced by the seed laser coupled between the ground state of 5S 1/2 and the first excited state of 5P 3/2 . A dip in the FWM spectrum was obtained for three-photon resonance due to V-type two-photon coherence using the pump and seed lasers. From the FWM spectra obtained for varying frequency detuning and seed-laser power, we determined that the seed laser acts as a stimulator for FWM generation, but also acts as a disturber of FWM due to V-type two-photon coherence.
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ERIC Educational Resources Information Center
Lester, Leanne; Waters, Stacey; Cross, Donna
2013-01-01
During the transition from primary to secondary school, students typically experience a new social environment, moving from primary school with small intact classes throughout the day with one main teacher, to a larger secondary school with teachers, classrooms and often classmates changing throughout the day. During this time, students report a…
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Paths to Success in Young Adulthood from Mental Health and Life Transitions in Emerging Adulthood
ERIC Educational Resources Information Center
Howard, Andrea L.; Galambos, Nancy L.; Krahn, Harvey J.
2010-01-01
This study followed a school-based sample (N = 920) to explore how trajectories of depressive symptoms and expressed anger from age 18 to 25, along with important life transitions, predicted life and career satisfaction at age 32. A two-group (women and men) bivariate growth model revealed that higher depressive symptoms at age 18 predicted lower…
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Tsuzuki, Manabu
2015-03-30
This study investigated types of career choice in high school students and examined the effects of career paths on time perspective development. The participants were 4,756 third grade students from nine public high schools in Tokyo. The high school questionnaire survey was conducted throughout autumn of 2008, 2009, and 2010. One year later, 962 graduates participated in the follow-up questionnaire survey by post. Distinguishing gender difference among career paths was found. Girls tend to choose significantly shorter learning careers (p < .01), for example junior college or vocational school in comparison to boys. Career indecision, i.e., students who could not set a concrete future career in high school, had significantly more negative time perspective than other groups (p < .05), which was caused by a deficiency of their basic cognitive ability. Longitudinal data showed different patterns of fluctuation in time perspective between "school to school transition" and "school to work transition". It is suggested that the "school to work transition" tends to be more critical for adolescents and has negative effects on time perspective. These results suggest that the goal content in careers may promote or inhibit the formation of time perspectives during the graduation transition.
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NASA Astrophysics Data System (ADS)
Nikitin, A. V.; Daumont, L.; Thomas, X.; Régalia, L.; Rey, M.; Tyuterev, Vl. G.; Brown, L. R.
2011-07-01
New measurements and assignments for the rovibrational transitions of the hot band 2 v3- v4 of 12CH 4 are reported from 4600 to 4880 cm -1 and refer to lower part of the 2 μm methane transparency window. Three long-path spectra were recorded with a Fourier transform spectrometer (FTS) in Reims using an L = 1603 m absorption path length at 1, 7, 34 h Pa for the natural samples of CH 4; a spectrum of enriched 13CH 4 was also used. Assignments were made for 196 lines of 2 v3(F 2,E)- v4. These transitions had an integrated intensity of 5 × 10 -24 cm/molecule at 296 K and improved the overall description of absorption in the 2.1 μm region. The empirical upper state levels of these assignments belong to Tetradecad (4800-6200 cm -1). The new analysis provided much better accuracies of badly blended positions of 2 v3(F 2)-ground state manifolds at 1.66 μm.
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Nivaskumar, Mangayarkarasi; Bouvier, Guillaume; Campos, Manuel; Nadeau, Nathalie; Yu, Xiong; Egelman, Edward H; Nilges, Michael; Francetic, Olivera
2014-05-06
The closely related bacterial type II secretion (T2S) and type IV pilus (T4P) systems are sophisticated machines that assemble dynamic fibers promoting protein transport, motility, or adhesion. Despite their essential role in virulence, the molecular mechanisms underlying helical fiber assembly remain unknown. Here, we use electron microscopy and flexible modeling to study conformational changes of PulG pili assembled by the Klebsiella oxytoca T2SS. Neural network analysis of 3,900 pilus models suggested a transition path toward low-energy conformations driven by progressive increase in fiber helical twist. Detailed predictions of interprotomer contacts along this path were tested by site-directed mutagenesis, pilus assembly, and protein secretion analyses. We demonstrate that electrostatic interactions between adjacent protomers (P-P+1) in the membrane drive pseudopilin docking, while P-P+3 and P-P+4 contacts determine downstream fiber stabilization steps. These results support a model of a spool-like assembly mechanism for fibers of the T2SS-T4P superfamily. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Nivaskumar, Mangayarkarasi; Bouvier, Guillaume; Campos, Manuel; Nadeau, Nathalie; Yu, Xiong; Egelman, Edward H.; Nilges, Michael; Francetic, Olivera
2014-01-01
SUMMARY The closely related bacterial type II secretion (T2S) and type IV pilus (T4P) systems are sophisticated machines that assemble dynamic fibers promoting protein transport, motility or adhesion. Despite their essential role in virulence, the molecular mechanisms underlying helical fiber assembly remain unknown. Here we use electron microscopy and flexible modeling to study conformational changes of PulG pili assembled by the Klebsiella oxytoca T2SS. Neural network analysis of 3900 pilus models suggested a transition path towards low-energy conformations driven by progressive increase in fiber helical twist. Detailed predictions of inter-protomer contacts along this path were tested by site-directed mutagenesis, pilus assembly and protein secretion analyses. We demonstrate that electrostatic interactions between adjacent protomers (P-P+1) in the membrane drive pseudopilin docking, while P-P+3 and P-P+4 contacts determine downstream fiber stabilization steps. These results support a new model of a spool-like assembly mechanism for fibers of the T2SS-T4P superfamily. PMID:24685147
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NASA Astrophysics Data System (ADS)
Kadoura, Ahmad; Sun, Shuyu; Salama, Amgad
2014-08-01
Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system's potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide.
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Feature selection for the classification of traced neurons.
López-Cabrera, José D; Lorenzo-Ginori, Juan V
2018-06-01
The great availability of computational tools to calculate the properties of traced neurons leads to the existence of many descriptors which allow the automated classification of neurons from these reconstructions. This situation determines the necessity to eliminate irrelevant features as well as making a selection of the most appropriate among them, in order to improve the quality of the classification obtained. The dataset used contains a total of 318 traced neurons, classified by human experts in 192 GABAergic interneurons and 126 pyramidal cells. The features were extracted by means of the L-measure software, which is one of the most used computational tools in neuroinformatics to quantify traced neurons. We review some current feature selection techniques as filter, wrapper, embedded and ensemble methods. The stability of the feature selection methods was measured. For the ensemble methods, several aggregation methods based on different metrics were applied to combine the subsets obtained during the feature selection process. The subsets obtained applying feature selection methods were evaluated using supervised classifiers, among which Random Forest, C4.5, SVM, Naïve Bayes, Knn, Decision Table and the Logistic classifier were used as classification algorithms. Feature selection methods of types filter, embedded, wrappers and ensembles were compared and the subsets returned were tested in classification tasks for different classification algorithms. L-measure features EucDistanceSD, PathDistanceSD, Branch_pathlengthAve, Branch_pathlengthSD and EucDistanceAve were present in more than 60% of the selected subsets which provides evidence about their importance in the classification of this neurons. Copyright © 2018 Elsevier B.V. All rights reserved.
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Traveling salesman problem with a center.
Lipowski, Adam; Lipowska, Dorota
2005-06-01
We study a traveling salesman problem where the path is optimized with a cost function that includes its length L as well as a certain measure C of its distance from the geometrical center of the graph. Using simulated annealing (SA) we show that such a problem has a transition point that separates two phases differing in the scaling behavior of L and C, in efficiency of SA, and in the shape of minimal paths.
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Transitioning DARPA Technology
2001-05-01
logo suggests, the Institute’s work reflects the summation of technology’s effects on business and government. With a reputation for fierce objectivity... effective for "customerpull" strategies. b. Products moved along the DIS path 30 percent of the time. This path was particularlysuccessful for small...must often be "waited out." But DARPA ha s few effective mechanisms for continuing to "market" its products after the prog ram is over- particularly
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Gradient Echo Quantum Memory in Warm Atomic Vapor
Pinel, Olivier; Hosseini, Mahdi; Sparkes, Ben M.; Everett, Jesse L.; Higginbottom, Daniel; Campbell, Geoff T.; Lam, Ping Koy; Buchler, Ben C.
2013-01-01
Gradient echo memory (GEM) is a protocol for storing optical quantum states of light in atomic ensembles. The primary motivation for such a technology is that quantum key distribution (QKD), which uses Heisenberg uncertainty to guarantee security of cryptographic keys, is limited in transmission distance. The development of a quantum repeater is a possible path to extend QKD range, but a repeater will need a quantum memory. In our experiments we use a gas of rubidium 87 vapor that is contained in a warm gas cell. This makes the scheme particularly simple. It is also a highly versatile scheme that enables in-memory refinement of the stored state, such as frequency shifting and bandwidth manipulation. The basis of the GEM protocol is to absorb the light into an ensemble of atoms that has been prepared in a magnetic field gradient. The reversal of this gradient leads to rephasing of the atomic polarization and thus recall of the stored optical state. We will outline how we prepare the atoms and this gradient and also describe some of the pitfalls that need to be avoided, in particular four-wave mixing, which can give rise to optical gain. PMID:24300586