Hamiltonian approach to Ehrenfest expectation values and Gaussian quantum states

PubMed Central

Bonet-Luz, Esther

2016-01-01

The dynamics of quantum expectation values is considered in a geometric setting. First, expectation values of the canonical observables are shown to be equivariant momentum maps for the action of the Heisenberg group on quantum states. Then, the Hamiltonian structure of Ehrenfest’s theorem is shown to be Lie–Poisson for a semidirect-product Lie group, named the Ehrenfest group. The underlying Poisson structure produces classical and quantum mechanics as special limit cases. In addition, quantum dynamics is expressed in the frame of the expectation values, in which the latter undergo canonical Hamiltonian motion. In the case of Gaussian states, expectation values dynamics couples to second-order moments, which also enjoy a momentum map structure. Eventually, Gaussian states are shown to possess a Lie–Poisson structure associated with another semidirect-product group, which is called the Jacobi group. This structure produces the energy-conserving variant of a class of Gaussian moment models that have previously appeared in the chemical physics literature. PMID:27279764

Ultrafast Hydration Dynamics and Coupled Water-Protein Fluctuations in Apomyoglobin

NASA Astrophysics Data System (ADS)

Yang, Yi; Zhang, Luyuan; Wang, Lijuan; Zhong, Dongping

2009-06-01

Protein hydration dynamics are of fundamental importance to its structure and function. Here, we characterize the global solvation dynamics and anisotropy dynamics around the apomyoglobin surface in different conformational states (native and molten globule) by measuring the Stokes shift and anisotropy decay of tryptophan with femtosecond-resolved fluorescence upconversion. With site-directed mutagenesis, we designed sixteen mutants with one tryptophan in each, and placed the probe at a desirable position ranging from buried in the protein core to fully solvent-exposed on the protein surface. In all protein sites studied, two distinct solvation relaxations (1-8 ps and 20-200 ps) were observed, reflecting the initial collective water relaxation and subsequent hydrogen-bond network restructuring, respectively, and both are strongly correlated with protein's local structures and chemical properties. The hydration dynamics of the mutants in molten globule state are faster than those observed in native state, indicating that the protein becomes more flexible and less structured when its conformation is converted from fully-folded native state to partially-folded molten globule state. Complementary, fluorescence anisotropy dynamics of all mutants in native state show an increasing trend of wobbling times (40-260 ps) when the location of the probe is changed from a loop, to a lateral helix, and then, to the compact protein core. Such an increase in wobbling times is related to the local protein structural rigidity, which relates the interaction of water with side chains. The ultrafast hydration dynamics and related side-chain motion around the protein surface unravel the coupled water-protein fluctuations on the picosecond time scales and indicate that the local protein motions are slaved by hydrating water fluctuations.

Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2012-04-10

To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example

NASA Astrophysics Data System (ADS)

Lerner, Eitan; Ingargiola, Antonino; Weiss, Shimon

2018-03-01

Bio-macromolecules carry out complicated functions through structural changes. To understand their mechanism of action, the structure of each step has to be characterized. While classical structural biology techniques allow the characterization of a few "structural snapshots" along the enzymatic cycle (usually of stable conformations), they do not cover all (and often fast interconverting) structures in the ensemble, where each may play an important functional role. Recently, several groups have demonstrated that structures of different conformations in solution could be solved by measuring multiple distances between different pairs of residues using single-molecule Förster resonance energy transfer (smFRET) and using them as constrains for hybrid/integrative structural modeling. However, this approach is limited in cases where the conformational dynamics is faster than the technique's temporal resolution. In this study, we combine existing tools that elucidate sub-millisecond conformational dynamics together with hybrid/integrative structural modeling to study the conformational states of the transcription bubble in the bacterial RNA polymerase-promoter open complex (RPo). We measured microsecond alternating laser excitation-smFRET of differently labeled lacCONS promoter dsDNA constructs. We used a combination of burst variance analysis, photon-by-photon hidden Markov modeling, and the FRET-restrained positioning and screening approach to identify two conformational states for RPo. The experimentally derived distances of one conformational state match the known crystal structure of bacterial RPo. The experimentally derived distances of the other conformational state have characteristics of a scrunched RPo. These findings support the hypothesis that sub-millisecond dynamics in the transcription bubble are responsible for transcription start site selection.

Characterizing RNA Dynamics at Atomic Resolution Using Solution-state NMR Spectroscopy

PubMed Central

Bothe, Jameson R.; Nikolova, Evgenia N.; Eichhorn, Catherine D.; Chugh, Jeetender; Hansen, Alexandar L.; Al-Hashimi, Hashim M.

2012-01-01

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering. PMID:22036746

Stuck in a State of Inattention? Functional Hyperconnectivity as an Indicator of Disturbed Intrinsic Brain Dynamics in Adolescents With Concussion: A Pilot Study

PubMed Central

Virji-Babul, Naznin

2018-01-01

Sports-related concussion in youth is a major public health issue. Evaluating the diffuse and often subtle changes in structure and function that occur in the brain, particularly in this population, remains a significant challenge. The goal of this pilot study was to evaluate the relationship between the intrinsic dynamics of the brain using resting-state functional magnetic resonance imaging (rs-fMRI) and relate these findings to structural brain correlates from diffusion tensor imaging in a group of adolescents with sports-related concussions (n = 6) and a group of healthy adolescent athletes (n = 6). We analyzed rs-fMRI data using a sliding windows approach and related the functional findings to structural brain correlates by applying graph theory analysis to the diffusion tensor imaging data. Within the resting-state condition, we extracted three separate brain states in both groups. Our analysis revealed that the brain dynamics in healthy adolescents was characterized by a dynamic pattern, shifting equally between three brain states; however, in adolescents with concussion, the pattern was more static with a longer time spent in one brain state. Importantly, this lack of dynamic flexibility in the concussed group was associated with increased nodal strength in the left middle frontal gyrus, suggesting reorganization in a region related to attention. This preliminary report shows that both the intrinsic brain dynamics and structural organization are altered in networks related to attention in adolescents with concussion. This first report in adolescents will be used to inform future studies in a larger cohort. PMID:29357675

Stuck in a State of Inattention? Functional Hyperconnectivity as an Indicator of Disturbed Intrinsic Brain Dynamics in Adolescents With Concussion: A Pilot Study.

PubMed

Muller, Angela M; Virji-Babul, Naznin

2018-01-01

Sports-related concussion in youth is a major public health issue. Evaluating the diffuse and often subtle changes in structure and function that occur in the brain, particularly in this population, remains a significant challenge. The goal of this pilot study was to evaluate the relationship between the intrinsic dynamics of the brain using resting-state functional magnetic resonance imaging (rs-fMRI) and relate these findings to structural brain correlates from diffusion tensor imaging in a group of adolescents with sports-related concussions ( n = 6) and a group of healthy adolescent athletes ( n = 6). We analyzed rs-fMRI data using a sliding windows approach and related the functional findings to structural brain correlates by applying graph theory analysis to the diffusion tensor imaging data. Within the resting-state condition, we extracted three separate brain states in both groups. Our analysis revealed that the brain dynamics in healthy adolescents was characterized by a dynamic pattern, shifting equally between three brain states; however, in adolescents with concussion, the pattern was more static with a longer time spent in one brain state. Importantly, this lack of dynamic flexibility in the concussed group was associated with increased nodal strength in the left middle frontal gyrus, suggesting reorganization in a region related to attention. This preliminary report shows that both the intrinsic brain dynamics and structural organization are altered in networks related to attention in adolescents with concussion. This first report in adolescents will be used to inform future studies in a larger cohort.

Investigation of Rhodopsin Dynamics in its Signaling State by Solid-State Deuterium NMR Spectroscopy

PubMed Central

Struts, Andrey V.; Chawla, Udeep; Perera, Suchithranga M.D.C.; Brown, Michael F.

2017-01-01

Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state 2H NMR spectral studies of aligned membrane samples of rhodopsin with selectively labeled retinal provide information on structural changes of the chromophore in different protein states. In addition, solid-state 2H NMR relaxation time measurements allow one to study the dynamics of the ligand during the transition from the inactive to the active state. Here we describe the methodological aspects of solid-state 2H NMR spectroscopy for functional studies of rhodopsin, with an emphasis on the dynamics of the retinal cofactor. We provide complete protocols for the preparation of NMR samples of rhodopsin with 11-cis-retinal selectively deuterated at the methyl groups in aligned membranes. In addition, we review optimized conditions for trapping the rhodopsin photointermediates; and lastly we address the challenging problem of trapping the signaling state of rhodopsin in aligned membrane films. PMID:25697522

Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings.

PubMed

Cole, Casey A; Mukhopadhyay, Rishi; Omar, Hanin; Hennig, Mirko; Valafar, Homayoun

2016-04-12

Residual dipolar couplings (RDCs) acquired by nuclear magnetic resonance (NMR) spectroscopy are an indispensable source of information in investigation of molecular structures and dynamics. Here, we present a comprehensive strategy for structure calculation and reconstruction of discrete-state dynamics from RDC data that is based on the singular value decomposition (SVD) method of order tensor estimation. In addition to structure determination, we provide a mechanism of producing an ensemble of conformations for the dynamical regions of a protein from RDC data. The developed methodology has been tested on simulated RDC data with ±1 Hz of error from an 83 residue α protein (PDB ID 1A1Z ) and a 213 residue α/β protein DGCR8 (PDB ID 2YT4 ). In nearly all instances, our method reproduced the structure of the protein including the conformational ensemble to within less than 2 Å. On the basis of our investigations, arc motions with more than 30° of rotation are identified as internal dynamics and are reconstructed with sufficient accuracy. Furthermore, states with relative occupancies above 20% are consistently recognized and reconstructed successfully. Arc motions with a magnitude of 15° or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions within the context of ±1 Hz of error.

Collective dynamics in heterogeneous networks of neuronal cellular automata

NASA Astrophysics Data System (ADS)

Manchanda, Kaustubh; Bose, Amitabha; Ramaswamy, Ramakrishna

2017-12-01

We examine the collective dynamics of heterogeneous random networks of model neuronal cellular automata. Each automaton has b active states, a single silent state and r - b - 1 refractory states, and can show 'spiking' or 'bursting' behavior, depending on the values of b. We show that phase transitions that occur in the dynamical activity can be related to phase transitions in the structure of Erdõs-Rényi graphs as a function of edge probability. Different forms of heterogeneity allow distinct structural phase transitions to become relevant. We also show that the dynamics on the network can be described by a semi-annealed process and, as a result, can be related to the Boolean Lyapunov exponent.

Advanced solid-state NMR techniques for characterization of membrane protein structure and dynamics: Application to Anabaena Sensory Rhodopsin

NASA Astrophysics Data System (ADS)

Ward, Meaghan E.; Brown, Leonid S.; Ladizhansky, Vladimir

2015-04-01

Studies of the structure, dynamics, and function of membrane proteins (MPs) have long been considered one of the main applications of solid-state NMR (SSNMR). Advances in instrumentation, and the plethora of new SSNMR methodologies developed over the past decade have resulted in a number of high-resolution structures and structural models of both bitopic and polytopic α-helical MPs. The necessity to retain lipids in the sample, the high proportion of one type of secondary structure, differential dynamics, and the possibility of local disorder in the loop regions all create challenges for structure determination. In this Perspective article we describe our recent efforts directed at determining the structure and functional dynamics of Anabaena Sensory Rhodopsin, a heptahelical transmembrane (7TM) protein. We review some of the established and emerging methods which can be utilized for SSNMR-based structure determination, with a particular focus on those used for ASR, a bacterial protein which shares its 7TM architecture with G-protein coupled receptors.

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born–Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersionmore » of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.« less

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

DOE PAGES

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert; ...

2017-05-24

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born–Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersionmore » of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.« less

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

NASA Astrophysics Data System (ADS)

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert; van Driel, Tim B.; Chollet, Matthieu; Glownia, James M.; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Matar, Samir F.; Nielsen, Martin M.; Benfatto, Maurizio; Gaffney, Kelly J.; Collet, Eric; Cammarata, Marco

2017-05-01

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born-Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersion of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.

Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

PubMed

Cheng, Chi-Yuan; Han, Songi

2013-01-01

Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

Inferring the relative resilience of alternative states

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Rojo, Carmen; Alvarez-Cobelas, Miguel; Rodrigo, Maria A.; Sanchez-Carrillo, Salvador

2013-01-01

Ecological systems may occur in alternative states that differ in ecological structures, functions and processes. Resilience is the measure of disturbance an ecological system can absorb before changing states. However, how the intrinsic structures and processes of systems that characterize their states affects their resilience remains unclear. We analyzed time series of phytoplankton communities at three sites in a floodplain in central Spain to assess the dominant frequencies or “temporal scales” in community dynamics and compared the patterns between a wet and a dry alternative state. The identified frequencies and cross-scale structures are expected to arise from positive feedbacks that are thought to reinforce processes in alternative states of ecological systems and regulate emergent phenomena such as resilience. Our analyses show a higher species richness and diversity but lower evenness in the dry state. Time series modeling revealed a decrease in the importance of short-term variability in the communities, suggesting that community dynamics slowed down in the dry relative to the wet state. The number of temporal scales at which community dynamics manifested, and the explanatory power of time series models, was lower in the dry state. The higher diversity, reduced number of temporal scales and the lower explanatory power of time series models suggest that species dynamics tended to be more stochastic in the dry state. From a resilience perspective our results highlight a paradox: increasing species richness may not necessarily enhance resilience. The loss of cross-scale structure (i.e. the lower number of temporal scales) in community dynamics across sites suggests that resilience erodes during drought. Phytoplankton communities in the dry state are therefore likely less resilient than in the wet state. Our case study demonstrates the potential of time series modeling to assess attributes that mediate resilience. The approach is useful for assessing resilience of alternative states across ecological and other complex systems.

Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation

PubMed Central

Wen, Han; Qin, Feng; Zheng, Wenjun

2016-01-01

As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state vs. the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel. PMID:27699868

Robust fixed order dynamic compensation for large space structure control

NASA Technical Reports Server (NTRS)

Calise, Anthony J.; Byrns, Edward V., Jr.

1989-01-01

A simple formulation for designing fixed order dynamic compensators which are robust to both uncertainty at the plant input and structured uncertainty in the plant dynamics is presented. The emphasis is on designing low order compensators for systems of high order. The formulation is done in an output feedback setting which exploits an observer canonical form to represent the compensator dynamics. The formulation also precludes the use of direct feedback of the plant output. The main contribution lies in defining a method for penalizing the states of the plant and of the compensator, and for choosing the distribution on initial conditions so that the loop transfer matrix approximates that of a full state design. To improve robustness to parameter uncertainty, the formulation avoids the introduction of sensitivity states, which has led to complex formulations in earlier studies where only structured uncertainty has been considered.

Control of complex networks requires both structure and dynamics

NASA Astrophysics Data System (ADS)

Gates, Alexander J.; Rocha, Luis M.

2016-04-01

The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics.

The structural, electronic and dynamic properties of the L1{sub 2}- type Co{sub 3}Ti alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arikan, Nihat; Özduran, Mustafa

2014-10-06

The structural, electronic and dynamic properties of the cubic Co{sub 3}Ti alloy in L1{sub 2} structure have been investigated using a pseudopotential plane wave (PP-PW) method within the generalized gradient approximation proposed by Perdew–Burke–Ernzerhof (GGA-PBE). The structural properties, including the lattice constant, the bulk modulus and its pressure derivative agree reasonably with the previous results. The density of state (DOS), projected density of state (PDOS) and electronic band structure are also reported. The DOS shows that Co{sub 3}Ti alloy has a metallic character since the energy bands cross the Fermi level. The density of states at Fermi level mainly comesmore » from the Co-3d states. Phonon dispersion curves and their corresponding total densities of states were obtained using a linear response in the framework of the density functional perturbation theory. All computed phonon frequencies are no imaginer and thus, Co{sub 3}Ti alloy is dynamically stable. The zone center phonon modes have been founded to be 9.307, 9.626 and 13.891 THz for Co{sub 3}Ti.« less

Markov State Models Provide Insights into Dynamic Modulation of Protein Function

PubMed Central

2015-01-01

Conspectus Protein function is inextricably linked to protein dynamics. As we move from a static structural picture to a dynamic ensemble view of protein structure and function, novel computational paradigms are required for observing and understanding conformational dynamics of proteins and its functional implications. In principle, molecular dynamics simulations can provide the time evolution of atomistic models of proteins, but the long time scales associated with functional dynamics make it difficult to observe rare dynamical transitions. The issue of extracting essential functional components of protein dynamics from noisy simulation data presents another set of challenges in obtaining an unbiased understanding of protein motions. Therefore, a methodology that provides a statistical framework for efficient sampling and a human-readable view of the key aspects of functional dynamics from data analysis is required. The Markov state model (MSM), which has recently become popular worldwide for studying protein dynamics, is an example of such a framework. In this Account, we review the use of Markov state models for efficient sampling of the hierarchy of time scales associated with protein dynamics, automatic identification of key conformational states, and the degrees of freedom associated with slow dynamical processes. Applications of MSMs for studying long time scale phenomena such as activation mechanisms of cellular signaling proteins has yielded novel insights into protein function. In particular, from MSMs built using large-scale simulations of GPCRs and kinases, we have shown that complex conformational changes in proteins can be described in terms of structural changes in key structural motifs or “molecular switches” within the protein, the transitions between functionally active and inactive states of proteins proceed via multiple pathways, and ligand or substrate binding modulates the flux through these pathways. Finally, MSMs also provide a theoretical toolbox for studying the effect of nonequilibrium perturbations on conformational dynamics. Considering that protein dynamics in vivo occur under nonequilibrium conditions, MSMs coupled with nonequilibrium statistical mechanics provide a way to connect cellular components to their functional environments. Nonequilibrium perturbations of protein folding MSMs reveal the presence of dynamically frozen glass-like states in their conformational landscape. These frozen states are also observed to be rich in β-sheets, which indicates their possible role in the nucleation of β-sheet rich aggregates such as those observed in amyloid-fibril formation. Finally, we describe how MSMs have been used to understand the dynamical behavior of intrinsically disordered proteins such as amyloid-β, human islet amyloid polypeptide, and p53. While certainly not a panacea for studying functional dynamics, MSMs provide a rigorous theoretical foundation for understanding complex entropically dominated processes and a convenient lens for viewing protein motions. PMID:25625937

Dynamics and control of twisting bi-stable structures

NASA Astrophysics Data System (ADS)

Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.

2018-02-01

Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states of the bi-stable twisting I-beam structures. The obtained optimal piezoelectric actuator positioning is not necessarily intuitive and when used with the proposed dynamic actuation strategy serve as a blueprint for the actuation of such multi-stable compliant structures to produce fast and large deflections with highly embeddable actuators. This class of structures has potential applications in aerospace systems and soft/compliant robotics.

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene

NASA Astrophysics Data System (ADS)

Ukpong, A. M.; Chetty, N.

2012-07-01

We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands.

Metastable structures and size effects in small group dynamics

PubMed Central

Lauro Grotto, Rosapia; Guazzini, Andrea; Bagnoli, Franco

2014-01-01

In his seminal works on group dynamics Bion defined a specific therapeutic setting allowing psychoanalytic observations on group phenomena. In describing the setting he proposed that the group was where his voice arrived. This physical limit was later made operative by assuming that the natural dimension of a therapeutic group is around 12 people. Bion introduced a theory of the group aspects of the mind in which proto-mental individual states spontaneously evolve into shared psychological states that are characterized by a series of features: (1) they emerge as a consequence of the natural tendency of (both conscious and unconscious) emotions to combine into structured group patterns; (2) they have a certain degree of stability in time; (3) they tend to alternate so that the dissolution of one is rapidly followed by the emergence of another; (4) they can be described in qualitative terms according to the nature of the emotional mix that dominates the state, in structural terms by a kind of typical “leadership” pattern, and in “cognitive” terms by a set of implicit expectations that are helpful in explaining the group behavior (i.e., the group behaves “as if” it was assuming that). Here we adopt a formal approach derived from Socio-physics in order to explore some of the structural and dynamic properties of this small group dynamics. We will described data from an analytic DS model simulating small group interactions of agents endowed with a very simplified emotional and cognitive dynamic in order to assess the following main points: (1) are metastable collective states allowed to emerge in the model and if so, under which conditions in the parameter space? (2) can these states be differentiated in structural terms? (3) to what extent are the emergent dynamic features of the systems dependent of the system size? We will finally discuss possible future applications of the quantitative descriptions of the interaction structure in the small group clinical setting. PMID:25071665

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

NASA Astrophysics Data System (ADS)

Li, Maozhi; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Ho, Kai-Ming

2008-05-01

Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of β relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of β relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long time scale.

Dynamic functional connectivity using state-based dynamic community structure: method and application to opioid analgesia.

PubMed

Robinson, Lucy F; Atlas, Lauren Y; Wager, Tor D

2015-03-01

We present a new method, State-based Dynamic Community Structure, that detects time-dependent community structure in networks of brain regions. Most analyses of functional connectivity assume that network behavior is static in time, or differs between task conditions with known timing. Our goal is to determine whether brain network topology remains stationary over time, or if changes in network organization occur at unknown time points. Changes in network organization may be related to shifts in neurological state, such as those associated with learning, drug uptake or experimental conditions. Using a hidden Markov stochastic blockmodel, we define a time-dependent community structure. We apply this approach to data from a functional magnetic resonance imaging experiment examining how contextual factors influence drug-induced analgesia. Results reveal that networks involved in pain, working memory, and emotion show distinct profiles of time-varying connectivity. Copyright © 2014 Elsevier Inc. All rights reserved.

Evolution of Excited-State Dynamics in Periodic Au 28, Au 36, Au 44, and Au 52 Nanoclusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Meng; Zeng, Chenjie; Sfeir, Matthew Y.

An understanding of the correlation between the atomic structure and optical properties of gold nanoclusters is essential for exploration of their functionalities and applications involving light harvesting and electron transfer. We report the femto-nanosecond excited state dynamics of a periodic series of face-centered cubic (FCC) gold nanoclusters (including Au 28, Au 36, Au 44, and Au 52), which exhibit a set of unique features compared with other similar sized clusters. Molecular-like ultrafast S n → S 1 internal conversions (i.e., radiationless electronic transitions) are observed in the relaxation dynamics of FCC periodic series. Excited-state dynamics with near-HOMO–LUMO gap excitation lacksmore » ultrafast decay component, and only the structural relaxation dominates in the dynamical process, which proves the absence of core–shell relaxation. Interestingly, both the relaxation of the hot carriers and the band-edge carrier recombination become slower as the size increases. The evolution in excited-state properties of this FCC series offers new insight into the structure-dependent properties of metal nanoclusters, which will benefit their optical energy harvesting and photocatalytic applications.« less

Evolution of Excited-State Dynamics in Periodic Au 28, Au 36, Au 44, and Au 52 Nanoclusters

DOE PAGES

Zhou, Meng; Zeng, Chenjie; Sfeir, Matthew Y.; ...

2017-08-10

An understanding of the correlation between the atomic structure and optical properties of gold nanoclusters is essential for exploration of their functionalities and applications involving light harvesting and electron transfer. We report the femto-nanosecond excited state dynamics of a periodic series of face-centered cubic (FCC) gold nanoclusters (including Au 28, Au 36, Au 44, and Au 52), which exhibit a set of unique features compared with other similar sized clusters. Molecular-like ultrafast S n → S 1 internal conversions (i.e., radiationless electronic transitions) are observed in the relaxation dynamics of FCC periodic series. Excited-state dynamics with near-HOMO–LUMO gap excitation lacksmore » ultrafast decay component, and only the structural relaxation dominates in the dynamical process, which proves the absence of core–shell relaxation. Interestingly, both the relaxation of the hot carriers and the band-edge carrier recombination become slower as the size increases. The evolution in excited-state properties of this FCC series offers new insight into the structure-dependent properties of metal nanoclusters, which will benefit their optical energy harvesting and photocatalytic applications.« less

Theoretical investigation of the structural, electronic, dynamical and thermal properties of YSn3 and YPb3

NASA Astrophysics Data System (ADS)

Kılıçarslan, Aynur; Salmankurt, Bahadır; Duman, Sıtkı

2017-02-01

We have performed an ab initio study of the structural, electronic, dynamical and thermal properties of the cubic AuCu3-type YSn3 and YPb3 by using the density functional theory, plane-wave pseudopotential method and a linear response scheme, within the generalized gradient approximation. An analysis of the electronic density of states at the Fermi level is found to be governed by the p states of Sn and Pb atoms with some contributions from the d states of Y atoms. The obtained phonon figures indicate that these material are dynamically stable in the cubic structure. Due to the metallic behavior of the compounds, the calculated zone-center phonon modes are triply degenerate. Also the thermal properties have been examined.

Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imai, Mizue; Saio, Tomohide; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810

2016-01-22

Redox-dependent changes in the structure and dynamics of human cytochrome c (Cyt c) were investigated by solution NMR. We found significant structural changes in several regions, including residues 23–28 (loop 3), which were further corroborated by chemical shift differences between the reduced and oxidized states of Cyt c. These differences are essential for discriminating redox states in Cyt c by cytochrome c oxidase (CcO) during electron transfer reactions. Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments identified that the region around His33 undergoes conformational exchanges on the μs-ms timescale, indicating significant redox-dependent structural changes. Because His33 is not part of the interaction sitemore » for CcO, our data suggest that the dynamic properties of the region, which is far from the interaction site for CcO, contribute to conformational changes during electron transfer to CcO. - Highlights: • Solution structure and dynamics analysis for human Cyt c by NMR. • Structural changes responsible for the discrimination of the redox state in Cyt c. • Conformational exchange in the region outside of the interaction site for CcO. • Less flexibility and rigid structure of the interaction site on Cyt c for CcO.« less

Model reduction in a subset of the original states

NASA Technical Reports Server (NTRS)

Yae, K. H.; Inman, D. J.

1992-01-01

A model reduction method is investigated to provide a smaller structural dynamic model for subsequent structural control design. A structural dynamic model is assumed to be derived from finite element analysis. It is first converted into the state space form, and is further reduced by the internal balancing method. Through the co-ordinate transformation derived from the states that are deleted during reduction, the reduced model is finally expressed with the states that are members of the original states. Therefore, the states in the final reduced model represent the degrees of freedom of the nodes that are selected by the designer. The procedure provides a more practical implementation of model reduction for applications in which specific nodes, such as sensor and/or actuator attachment points, are to be retained in the reduced model. Thus, it ensures that the reduced model is under the same input and output condition as the original physical model. The procedure is applied to two simple examples and comparisons are made between the full and reduced order models. The method can be applied to a linear, continuous and time-invariant model of structural dynamics with nonproportional viscous damping.

Electrically tunable robust edge states in graphene-based topological photonic crystal slabs

NASA Astrophysics Data System (ADS)

Song, Zidong; Liu, HongJun; Huang, Nan; Wang, ZhaoLu

2018-03-01

Topological photonic crystals are optical structures supporting topologically protected unidirectional edge states that exhibit robustness against defects. Here, we propose a graphene-based all-dielectric photonic crystal slab structure that supports two-dimensionally confined topological edge states. These topological edge states can be confined in the out-of-plane direction by two parallel graphene sheets. In the structure, the excitation frequency range of topological edge states can be dynamically and continuously tuned by varying bias voltage across the two parallel graphene sheets. Utilizing this kind of architecture, we construct Z-shaped channels to realize topological edge transmission with diffrerent frequencies. The proposal provides a new degree of freedom to dynamically control topological edge states and potential applications for robust integrated photonic devices and optical communication systems.

Vibrational structure of the S 2 (1B u) excited state of diphenyloctatetraene observed by femtosecond stimulated Raman spectroscopy

NASA Astrophysics Data System (ADS)

Kukura, Philipp; McCamant, David W.; Davis, Paul H.; Mathies, Richard A.

2003-11-01

Femtosecond time-resolved stimulated Raman spectroscopy (FSRS) is used to study the vibrational structure and dynamics of the S 2 state of diphenyloctatetraene. Strong vibrational features at 1184, 1259 and 1578 cm -1 whose linewidths are determined by the S 2 electronic lifetime are observed at early times after photoexcitation at 397 nm. Kinetic analysis of the integrated Raman intensities as well as the transient absorption reveals an exponential decay of the S 2 state on the order of 100 fs. These results demonstrate the ability of FSRS to study the vibrational structure of excited state and chemical reaction dynamics on the femtosecond timescale.

Structure and dynamics of the influenza A M2 channel: a comparison of three structures.

PubMed

Leonov, Hadas; Arkin, Isaiah T

2009-11-01

The M2 protein is an essential component of the Influenza virus' infectivity cycle. It is a homo-tetrameric bundle forming a pH-gated H(+) channel. The structure of M2 was solved by three different groups, using different techniques, protein sequences and pH environment. For example, solid-state NMR spectroscopy was used on a protein in lipid bilayers, while X-ray crystallography and solution NMR spectroscopy were applied on a protein in detergent micelles. The resulting structures from the above efforts are rather distinct. Herein, we examine the different structures under uniform conditions such as a lipid bilayer and specified protonation state. We employ extensive molecular dynamics simulations, in several protonation states, representing both closed and open forms of the channel. Exploring the properties of each of these structures has shown that the X-ray structure is more stable than the other structures according to various criteria, although its water conductance and water-wire formation do not correlate to the protonation state of the channel.

Structural fluctuation governed dynamic diradical character in pentacene.

PubMed

Yang, Hongfang; Chen, Mengzhen; Song, Xinyu; Bu, Yuxiang

2015-06-07

We unravel intriguing dynamical diradical behavior governed by structural fluctuation in pentacene using ab initio molecular dynamics simulation. In contrast to static equilibrium configuration of pentacene with a closed-shell ground state without diradical character, due to structural fluctuation, some of its dynamical snapshot configurations exhibit an open-shell broken-symmetry singlet ground state with diradical character, and such diradical character presents irregular pulsing behavior in time evolution. Not all structural changes can lead to diradical character, only those involving the shortening of cross-linking C-C bonds and variations of the C-C bonds in polyacetylene chains are the main contributors. This scenario about diradicalization is distinctly different from that in long acenes. The essence is that structural distortion cooperatively raises the HOMO and lowers the LUMO, efficiently reducing the HOMO-LUMO and singlet-triplet energy gaps, which facilitate the formation of a broken-symmetry open-shell singlet state. The irregular pulsing behavior originates from the mixing of normal vibrations in pentacene. This fascinating behavior suggests the potential application of pentacene as a suitable building block in the design of new electronic devices due to its magnetism-controllability through energy induction. This work provides new insight into inherent electronic property fluctuation in acenes.

Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models.

PubMed

Rogers, Lauren A; Storvik, Geir O; Knutsen, Halvor; Olsen, Esben M; Stenseth, Nils C

2017-07-01

Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may have played a role in driving local dynamics. More generally, we demonstrated how state-space models can be used to test evidence for population spatial structure based on survey time-series data. Our study shows the importance of considering spatially structured dynamics, as the inferences from such an approach can lead to a different ecological understanding of the drivers of population declines, and fundamentally different management actions to restore populations. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

A Model Comparison for Characterizing Protein Motions from Structure

NASA Astrophysics Data System (ADS)

David, Charles; Jacobs, Donald

2011-10-01

A comparative study is made using three computational models that characterize native state dynamics starting from known protein structures taken from four distinct SCOP classifications. A geometrical simulation is performed, and the results are compared to the elastic network model and molecular dynamics. The essential dynamics is quantified by a direct analysis of a mode subspace constructed from ANM and a principal component analysis on both the FRODA and MD trajectories using root mean square inner product and principal angles. Relative subspace sizes and overlaps are visualized using the projection of displacement vectors on the model modes. Additionally, a mode subspace is constructed from PCA on an exemplar set of X-ray crystal structures in order to determine similarly with respect to the generated ensembles. Quantitative analysis reveals there is significant overlap across the three model subspaces and the model independent subspace. These results indicate that structure is the key determinant for native state dynamics.

MHD Simulation for Investigating the Dynamic State Transition Responsible for a Solar Eruption in Active Region 12158

NASA Astrophysics Data System (ADS)

Lee, Hwanhee; Magara, Tetsuya

2018-06-01

We present a magnetohydrodynamic model of solar eruption based on the dynamic state transition from the quasi-static state to the eruptive state of an active region (AR) magnetic field. For the quasi-static state before an eruption, we consider the existence of a slow solar wind originating from an AR, which may continuously make the AR magnetic field deviate from mechanical equilibrium. In this model, we perform a three-dimensional magnetohydrodynamic simulation of AR 12158 producing a coronal mass ejection, where the initial magnetic structure of the simulation is given by a nonlinear force-free field derived from an observed photospheric vector magnetic field. We then apply a pressure-driven outflow to the upper part of the magnetic structure to achieve a quasi-static pre-eruptive state. The simulation shows that the eruptive process observed in this AR may be caused by the dynamic state transition of an AR magnetic field, which is essentially different from the destabilization of a static magnetic field. The dynamic state transition is determined from the shape evolution of the magnetic field line according to the κH-mechanism. This work demonstrates how the mechanism works to produce a solar eruption in the dynamic solar corona governed by the gravitational field and the continuous outflows of solar wind.

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

PubMed Central

Kannan, Srinivasaraghavan; Zacharias, Martin

2014-01-01

The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures. PMID:24563686

Modeling repetitive motions using structured light.

PubMed

Xu, Yi; Aliaga, Daniel G

2010-01-01

Obtaining models of dynamic 3D objects is an important part of content generation for computer graphics. Numerous methods have been extended from static scenarios to model dynamic scenes. If the states or poses of the dynamic object repeat often during a sequence (but not necessarily periodically), we call such a repetitive motion. There are many objects, such as toys, machines, and humans, undergoing repetitive motions. Our key observation is that when a motion-state repeats, we can sample the scene under the same motion state again but using a different set of parameters; thus, providing more information of each motion state. This enables robustly acquiring dense 3D information difficult for objects with repetitive motions using only simple hardware. After the motion sequence, we group temporally disjoint observations of the same motion state together and produce a smooth space-time reconstruction of the scene. Effectively, the dynamic scene modeling problem is converted to a series of static scene reconstructions, which are easier to tackle. The varying sampling parameters can be, for example, structured-light patterns, illumination directions, and viewpoints resulting in different modeling techniques. Based on this observation, we present an image-based motion-state framework and demonstrate our paradigm using either a synchronized or an unsynchronized structured-light acquisition method.

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

PubMed

Karamzadeh, Razieh; Karimi-Jafari, Mohammad Hossein; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Salekdeh, Ghasem Hosseini; Moosavi-Movahedi, Ali Akbar

2017-06-16

The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are important for substrate binding and functional activities. Here, we address the redox-dependent conformational dynamics of hPDI through molecular dynamics (MD) simulations. Collective domain motions are identified by the principal component analysis of MD trajectories and redox-dependent opening-closing structure variations are highlighted on projected free energy landscapes. Then, important structural features that exhibit considerable differences in dynamics of redox states are extracted by statistical machine learning methods. Mapping the structural variations to time series of residue interaction networks also provides a holistic representation of the dynamical redox differences. With emphasizing on persistent long-lasting interactions, an approach is proposed that compiled these time series networks to a single dynamic residue interaction network (DRIN). Differential comparison of DRIN in oxidized and reduced states reveals chains of residue interactions that represent potential allosteric paths between catalytic and ligand binding sites of hPDI.

A model structure for identification of linear models of the UH-60 helicopter in hover and forward flight

DOT National Transportation Integrated Search

1995-08-01

A linear model structure applicable to identification of the UH-60 flight : dynamics in hover and forward flight without rotor-state data is developed. The : structure of the model is determined through consideration of the important : dynamic modes ...

An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase

PubMed Central

Matthes, Dirk; Gapsys, Vytautas; Brennecke, Julian T.; de Groot, Bert L.

2016-01-01

The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils. PMID:27616019

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

Communication: Smoothing out excited-state dynamics: Analytical gradients for dynamically weighted complete active space self-consistent field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glover, W. J., E-mail: williamjglover@gmail.com

2014-11-07

State averaged complete active space self-consistent field (SA-CASSCF) is a workhorse for determining the excited-state electronic structure of molecules, particularly for states with multireference character; however, the method suffers from known issues that have prevented its wider adoption. One issue is the presence of discontinuities in potential energy surfaces when a state that is not included in the state averaging crosses with one that is. In this communication I introduce a new dynamical weight with spline (DWS) scheme that mimics SA-CASSCF while removing energy discontinuities due to unweighted state crossings. In addition, analytical gradients for DWS-CASSCF (and other dynamically weightedmore » schemes) are derived for the first time, enabling energy-conserving excited-state ab initio molecular dynamics in instances where SA-CASSCF fails.« less

Dynamic Connectivity Patterns in Conscious and Unconscious Brain

PubMed Central

Ma, Yuncong; Hamilton, Christina

2017-01-01

Abstract Brain functional connectivity undergoes dynamic changes from the awake to unconscious states. However, how the dynamics of functional connectivity patterns are linked to consciousness at the behavioral level remains elusive. In this study, we acquired resting-state functional magnetic resonance imaging data during wakefulness and graded levels of consciousness in rats. Data were analyzed using a dynamic approach combining the sliding window method and k-means clustering. Our results demonstrate that whole-brain networks contained several quasi-stable patterns that dynamically recurred from the awake state into anesthetized states. Remarkably, two brain connectivity states with distinct spatial similarity to the structure of anatomical connectivity were strongly biased toward high and low consciousness levels, respectively. These results provide compelling neuroimaging evidence linking the dynamics of whole-brain functional connectivity patterns and states of consciousness at the behavioral level. PMID:27846731

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

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.

Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation.

PubMed

Wen, Han; Qin, Feng; Zheng, Wenjun

2016-12-01

As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state versus the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel. Proteins 2016; 84:1938-1949. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Analysis of the structure and dynamics of human serum albumin.

PubMed

Guizado, T R Cuya

2014-10-01

Human serum albumin (HSA) is a biologically relevant protein that binds a variety of drugs and other small molecules. No less than 50 structures are deposited in the RCSB Protein Data Bank (PDB). Based on these structures, we first performed a clustering analysis. Despite the diversity of ligands, only two well defined conformations are detected, with a deviation of 0.46 nm between the average structures of the two clusters, while deviations within each cluster are smaller than 0.08 nm. Those two conformations are representative of the apoprotein and the HSA-myristate complex already identified in previous literature. Considering the structures within each cluster as a representative sample of the dynamical states of the corresponding conformation, we scrutinize the structural and dynamical differences between both conformations. Analysis of the fluctuations within each cluster set reveals that domain II is the most rigid one and better matches both structures. Then, taking this domain as reference, we show that the structural difference between both conformations can be expressed in terms of twist and hinge motions of domains I and III, respectively. We also characterize the dynamical difference between conformations by computing correlations and principal components for each set of dynamical states. The two conformations display different collective motions. The results are compared with those obtained from the trajectories of short molecular dynamics simulations, giving consistent outcomes. Let us remark that, beyond the relevance of the results for the structural and dynamical characterization of HAS conformations, the present methodology could be extended to other proteins in the PDB archive.

Dynamic spectral structure specifies vowels for children and adultsa

PubMed Central

Nittrouer, Susan

2008-01-01

When it comes to making decisions regarding vowel quality, adults seem to weight dynamic syllable structure more strongly than static structure, although disagreement exists over the nature of the most relevant kind of dynamic structure: spectral change intrinsic to the vowel or structure arising from movements between consonant and vowel constrictions. Results have been even less clear regarding the signal components children use in making vowel judgments. In this experiment, listeners of four different ages (adults, and 3-, 5-, and 7-year-old children) were asked to label stimuli that sounded either like steady-state vowels or like CVC syllables which sometimes had middle sections masked by coughs. Four vowel contrasts were used, crossed for type (front/back or closed/open) and consonant context (strongly or only slightly constraining of vowel tongue position). All listeners recognized vowel quality with high levels of accuracy in all conditions, but children were disproportionately hampered by strong coarticulatory effects when only steady-state formants were available. Results clarified past studies, showing that dynamic structure is critical to vowel perception for all aged listeners, but particularly for young children, and that it is the dynamic structure arising from vocal-tract movement between consonant and vowel constrictions that is most important. PMID:17902868

Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

PubMed

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

2014-05-01

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suhara, Tadahiro; Kanada-En'yo, Yoshiko

Structures of excited states in {sup 14}C are investigated with a method of {beta}-{gamma} constraint antisymmetrized molecular dynamics in combination with the generator coordinate method. Various excited states with the developed 3{alpha}-cluster core structures are suggested in positive- and negative-parity states. In the positive-parity states, triaxial deformed and linear-chain structures are found to construct excited bands. Interestingly, {sup 10}Be+{alpha} correlation is found in the cluster states above the {sup 10}Be+{alpha} threshold energy.

Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy.

PubMed

Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy

2018-02-01

A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 3 10 -helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Dynamical pairwise entanglement and two-point correlations in the three-ligand spin-star structure

NASA Astrophysics Data System (ADS)

Motamedifar, M.

2017-10-01

We consider the three-ligand spin-star structure through homogeneous Heisenberg interactions (XXX-3LSSS) in the framework of dynamical pairwise entanglement. It is shown that the time evolution of the central qubit ;one-particle; state (COPS) brings about the generation of quantum W states at periodical time instants. On the contrary, W states cannot be generated from the time evolution of a ligand ;one-particle; state (LOPS). We also investigate the dynamical behavior of two-point quantum correlations as well as the expectation values of the different spin-components for each element in the XXX-3LSSS. It is found that when a W state is generated, the same value of the concurrence between any two arbitrary qubits arises from the xx and yy two-point quantum correlations. On the opposite, zz quantum correlation between any two qubits vanishes at these time instants.

Structure and dynamics of proflavine association around DNA.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2016-04-21

Proflavine is a small molecule that intercalates into DNA and, thereby, acts as an anticancer agent. Intercalation of proflavine is shown to be a two-step process in which the first step is believed to be the formation of a pre-intercalative outside bound state. Experimental studies so far have been unable to capture the nature of the outside bound state. However, the sub-millisecond timescale observed in fluorescence kinetic experiments is often attributed to the binding of proflavine outside of DNA. Here, we have performed molecular dynamics simulations with multiple proflavine molecules to study the structure and dynamics of the formation of the outside bound state of DNA at different ion concentrations. We observed that the timescale of the outside bound state formation is, at least, five orders of magnitude faster (in nanoseconds) than the experimentally reported timescale (sub-milliseconds) attributed to binding outside DNA. Moreover, we also observed the stacked arrangement of proflavine all around DNA, which is different from the experimentally predicted stacking arrangement perpendicular to the helical axis of DNA in the close vicinity of the phosphate groups. This study, therefore, provides insight into the molecular structure and dynamics of the pre-intercalative outside bound state and will help in understanding the overall intercalation mechanism.

ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics

NASA Astrophysics Data System (ADS)

Nibbering, Erik T. J.; Fidder, Henk; Pines, Ehud

2005-05-01

Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

NASA Astrophysics Data System (ADS)

Petrov, Yu V.; Inogamov, N. A.; Mokshin, A. V.; Galimzyanov, B. N.

2018-01-01

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman-Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo-Greenwood with the quantum molecular dynamics calculations.

From structure to function, via dynamics

NASA Astrophysics Data System (ADS)

Stetter, O.; Soriano, J.; Geisel, T.; Battaglia, D.

2013-01-01

Neurons in the brain are wired into a synaptic network that spans multiple scales, from local circuits within cortical columns to fiber tracts interconnecting distant areas. However, brain function require the dynamic control of inter-circuit interactions on time-scales faster than synaptic changes. In particular, strength and direction of causal influences between neural populations (described by the so-called directed functional connectivity) must be reconfigurable even when the underlying structural connectivity is fixed. Such directed functional influences can be quantified resorting to causal analysis of time-series based on tools like Granger Causality or Transfer Entropy. The ability to quickly reorganize inter-areal interactions is a chief requirement for performance in a changing natural environment. But how can manifold functional networks stem "on demand" from an essentially fixed structure? We explore the hypothesis that the self-organization of neuronal synchronous activity underlies the control of brain functional connectivity. Based on simulated and real recordings of critical neuronal cultures in vitro, as well as on mean-field and spiking network models of interacting brain areas, we have found that "function follows dynamics", rather than structure. Different dynamic states of a same structural network, characterized by different synchronization properties, are indeed associated to different functional digraphs (functional multiplicity). We also highlight the crucial role of dynamics in establishing a structure-to-function link, by showing that whenever different structural topologies lead to similar dynamical states, than the associated functional connectivities are also very similar (structural degeneracy).

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

PubMed

Villaverde, Alejandro F; Banga, Julio R

2017-11-01

The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability.

Wind Turbine Structural Dynamics

NASA Technical Reports Server (NTRS)

Miller, D. R. (Editor)

1978-01-01

A workshop on wind turbine structural dynamics was held to review and document current United States work on the dynamic behavior of large wind turbines, primarily of the horizontal-axis type, and to identify and discuss other wind turbine configurations that may have lower cost and weight. Information was exchanged on the following topics: (1) Methods for calculating dynamic loads; (2) Aeroelasticity stability (3) Wind loads, both steady and transient; (4) Critical design conditions; (5) Drive train dynamics; and (6) Behavior of operating wind turbines.

Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.

PubMed

Sen, Kakali; Horrell, Sam; Kekilli, Demet; Yong, Chin W; Keal, Thomas W; Atakisi, Hakan; Moreau, David W; Thorne, Robert E; Hough, Michael A; Strange, Richard W

2017-07-01

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp CAT and His CAT ) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp CAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile CAT ), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp CAT . A previously unobserved conformation of Ile CAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

The "Rust" Challenge: On the Correlations between Electronic Structure, Excited State Dynamics, and Photoelectrochemical Performance of Hematite Photoanodes for Solar Water Splitting.

PubMed

Grave, Daniel A; Yatom, Natav; Ellis, David S; Toroker, Maytal Caspary; Rothschild, Avner

2018-03-05

In recent years, hematite's potential as a photoanode material for solar hydrogen production has ignited a renewed interest in its physical and interfacial properties, which continues to be an active field of research. Research on hematite photoanodes provides new insights on the correlations between electronic structure, transport properties, excited state dynamics, and charge transfer phenomena, and expands our knowledge on solar cell materials into correlated electron systems. This research news article presents a snapshot of selected theoretical and experimental developments linking the electronic structure to the photoelectrochemical performance, with particular focus on optoelectronic properties and charge carrier dynamics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

PubMed

Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

2010-06-03

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

Molecular Dynamics Simulation of Bovine Pancreatic Ribonuclease A - CpA and Transition State-like Complexes

PubMed Central

Formoso, Elena; Matxain, Jon M.; Lopez, Xabier; York, Darrin M.

2010-01-01

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, in order to study the conformational dynamics, structural relaxation, and differential solvation that occurs at discreet stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics, and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogs. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3′,5′-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen bond patterns are presented and compared. The integrity of the overall backbone structure is preserved in the simulations, and support a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen bond donation to the non-bridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate, and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step. PMID:20455590

Ultrafast Structural Dynamics in Combustion Relevant Model Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Peter M.

2014-03-31

The research project explored the time resolved structural dynamics of important model reaction system using an array of novel methods that were developed specifically for this purpose. They include time resolved electron diffraction, time resolved relativistic electron diffraction, and time resolved Rydberg fingerprint spectroscopy. Toward the end of the funding period, we also developed time-resolved x-ray diffraction, which uses ultrafast x-ray pulses at LCLS. Those experiments are just now blossoming, as the funding period expired. In the following, the time resolved Rydberg Fingerprint Spectroscopy is discussed in some detail, as it has been a very productive method. The binding energymore » of an electron in a Rydberg state, that is, the energy difference between the Rydberg level and the ground state of the molecular ion, has been found to be a uniquely powerful tool to characterize the molecular structure. To rationalize the structure sensitivity we invoke a picture from electron diffraction: when it passes the molecular ion core, the Rydberg electron experiences a phase shift compared to an electron in a hydrogen atom. This phase shift requires an adjustment of the binding energy of the electron, which is measurable. As in electron diffraction, the phase shift depends on the molecular, geometrical structure, so that a measurement of the electron binding energy can be interpreted as a measurement of the molecule’s structure. Building on this insight, we have developed a structurally sensitive spectroscopy: the molecule is first elevated to the Rydberg state, and the binding energy is then measured using photoelectron spectroscopy. The molecule’s structure is read out as the binding energy spectrum. Since the photoionization can be done with ultrafast laser pulses, the technique is inherently capable of a time resolution in the femtosecond regime. For the purpose of identifying the structures of molecules during chemical reactions, and for the analysis of molecular species in the hot environments of combustion processes, there are several features that make the Rydberg ionization spectroscopy uniquely useful. First, the Rydberg electron’s orbit is quite large and covers the entire molecule for most molecular structures of combustion interest. Secondly, the ionization does not change vibrational quantum numbers, so that even complicated and large molecules can be observed with fairly well resolved spectra. In fact, the spectroscopy is blind to vibrational excitation of the molecule. This has the interesting consequence for the study of chemical dynamics, where the molecules are invariably very energetic, that the molecular structures are observed unobstructed by the vibrational congestion that dominates other spectroscopies. This implies also that, as a tool to probe the time-dependent structural dynamics of chemically interesting molecules, Rydberg spectroscopy may well be better suited than electron or x-ray diffraction. With recent progress in calculating Rydberg binding energy spectra, we are approaching the point where the method can be evolved into a structure determination method. To implement the Rydberg ionization spectroscopy we use a molecular beam based, time-resolved pump-probe multi-photon ionization/photoelectron scheme in which a first laser pulse excites the molecule to a Rydberg state, and a probe pulse ionizes the molecule. A time-of-flight detector measures the kinetic energy spectrum of the photoelectrons. The photoelectron spectrum directly provides the binding energy of the electron, and thereby reveals the molecule’s time-dependent structural fingerprint. Only the duration of the laser pulses limits the time resolution. With a new laser system, we have now reached time resolutions better than 100 fs, although very deep UV wavelengths (down to 190 nm) have slightly longer instrument functions. The structural dynamics of molecules in Rydberg-excited states is obtained by delaying the probe ionization photon from the pump photon; the structural dynamics of molecules in their ground state or excited valence states is measured by inducing the dynamics using a near UV laser pulse, and employing a multi-photon ionization scheme via the Rydberg states as a probe process. Thus, the technique is capable of measuring the reaction dynamics in any electronic state of neutral molecules.« less

Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

PubMed Central

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-01-01

The membrane-bound sodium–calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen–deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α1 and α2 repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na+ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins. PMID:27879668

Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins.

PubMed

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-11-22

The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca 2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca 2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca 2+ /cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.

Unsymmetric Lanczos model reduction and linear state function observer for flexible structures

NASA Technical Reports Server (NTRS)

Su, Tzu-Jeng; Craig, Roy R., Jr.

1991-01-01

This report summarizes part of the research work accomplished during the second year of a two-year grant. The research, entitled 'Application of Lanczos Vectors to Control Design of Flexible Structures' concerns various ways to use Lanczos vectors and Krylov vectors to obtain reduced-order mathematical models for use in the dynamic response analyses and in control design studies. This report presents a one-sided, unsymmetric block Lanczos algorithm for model reduction of structural dynamics systems with unsymmetric damping matrix, and a control design procedure based on the theory of linear state function observers to design low-order controllers for flexible structures.

Ion-ion dynamic structure factor, acoustic modes, and equation of state of two-temperature warm dense aluminum

NASA Astrophysics Data System (ADS)

Harbour, L.; Förster, G. D.; Dharma-wardana, M. W. C.; Lewis, Laurent J.

2018-04-01

The ion-ion dynamical structure factor and the equation of state of warm dense aluminum in a two-temperature quasiequilibrium state, with the electron temperature higher than the ion temperature, are investigated using molecular-dynamics simulations based on ion-ion pair potentials constructed from a neutral pseudoatom model. Such pair potentials based on density functional theory are parameter-free and depend directly on the electron temperature and indirectly on the ion temperature, enabling efficient computation of two-temperature properties. Comparison with ab initio simulations and with other average-atom calculations for equilibrium aluminum shows good agreement, justifying a study of quasiequilibrium situations. Analyzing the van Hove function, we find that ion-ion correlations vanish in a time significantly smaller than the electron-ion relaxation time so that dynamical properties have a physical meaning for the quasiequilibrium state. A significant increase in the speed of sound is predicted from the modification of the dispersion relation of the ion acoustic mode as the electron temperature is increased. The two-temperature equation of state including the free energy, internal energy, and pressure is also presented.

Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

PubMed Central

Miller, Bill R.; Parish, Carol A.; Wu, Eugene Y.

2014-01-01

During DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates. The dynamics of this process are crucial to the overall effectiveness of catalysis. Although X-ray crystal structures of DNA polymerase I with substrate dNTPs have revealed key structural states along the catalytic pathway, solution fluorescence studies indicate that those key states are populated in the absence of substrate. Herein, we report the first atomistic simulations showing the conformational changes between the closed, open, and ajar conformations of DNA polymerase I in the binary (enzyme∶DNA) state to better understand its dynamics. We have applied long time-scale, unbiased molecular dynamics to investigate the opening process of the fingers domain in the absence of substrate for B. stearothermophilis DNA polymerase in silico. These simulations are biologically and/or physiologically relevant as they shed light on the transitions between states in this important enzyme. All closed and ajar simulations successfully transitioned into the fully open conformation, which is known to be the dominant binary enzyme-DNA conformation from solution and crystallographic studies. Furthermore, we have detailed the key stages in the opening process starting from the open and ajar crystal structures, including the observation of a previously unknown key intermediate structure. Four backbone dihedrals were identified as important during the opening process, and their movements provide insight into the recognition of dNTP substrate molecules by the polymerase binary state. In addition to revealing the opening mechanism, this study also demonstrates our ability to study biological events of DNA polymerase using current computational methods without biasing the dynamics. PMID:25474643

Dynamically Switching the Polarization State of Light Based on the Phase Transition of Vanadium Dioxide

NASA Astrophysics Data System (ADS)

Jia, Zhi-Yong; Shu, Fang-Zhou; Gao, Ya-Jun; Cheng, Feng; Peng, Ru-Wen; Fan, Ren-Hao; Liu, Yongmin; Wang, Mu

2018-03-01

There have been great endeavors devoted to manipulating the polarization state of light by plasmonic nanostructures in recent decades. However, the topic of active polarizers has attracted much less attention. We present a composite plasmonic nanostructure consisting of vanadium dioxide that can dynamically modulate the polarization state of the reflected light through a thermally induced phase transition of vanadium dioxide. We design a system consisting of anisotropic plasmonic nanostructures with vanadium dioxide that exhibits distinct reflections subjected to different linearly polarized incidence at room temperature and in the heated state. Under a particular linearly polarized incidence, the polarization state of the reflected light changes at room temperature, and reverts to its original polarization state above the phase-transition temperature. The composite structure can also be used to realize a dynamically switchable infrared image, wherein a pattern can be visualized at room temperature while it disappears above the phase-transition temperature. The composite structure could be potentially used for versatile optical modulators, molecular detection, and polarimetric imaging.

Interaction of the Disordered Yersinia Effector Protein YopE with Its Cognate Chaperone SycE

DTIC Science & Technology

2009-01-01

structures of YopECBD were molten globules with a hydrophobic core. Molecular dynamics (MD) simulations indi- cated that the structure remained compact at...ensembles of unfolded conformations of the Yersinia effector YopE using REMD simulations and docked them to the chaper- one SycE using a multistep protein...disordered state but transitions into an ordered state upon binding to its cognate chaperone (7). The dynamics of the disordered effector protein and

Dynamics of internal pore opening in KV channels probed by a fluorescent unnatural amino acid

PubMed Central

Kalstrup, Tanja; Blunck, Rikard

2013-01-01

Atomic-scale models on the gating mechanism of voltage-gated potassium channels (Kv) are based on linear interpolations between static structures of their initial and final state derived from crystallography and molecular dynamics simulations, and, thus, lack dynamic structural information. The lack of information on dynamics and intermediate states makes it difficult to associate the structural with the dynamic functional data obtained with electrophysiology. Although voltage-clamp fluorometry fills this gap, it is limited to sites extracellularly accessible, when the key region for gating is located at the cytosolic side of the channels. Here, we solved this problem by performing voltage-clamp fluorometry with a fluorescent unnatural amino acid. By using an orthogonal tRNA-synthetase pair, the fluorescent unnatural amino acid was incorporated in the Shaker voltage-gated potassium channel at key regions that were previously inaccessible. Thus, we defined which parts act independently and which parts act cooperatively and found pore opening to occur in two sequential transitions. PMID:23630265

Steady state and dynamical structure of a cosmic-ray-modified termination shock

NASA Technical Reports Server (NTRS)

Donohue, D. J.; Zank, G. P.

1993-01-01

A hydrodynamic model is developed for the structure of a cosmic-ray-modified termination shock. The model is based on the two-fluid equations of diffuse shock acceleration (Drury and Volk, 1981). Both the steady state structure of the shock and its interaction with outer heliospheric disturbances are considered. Under the assumption that the solar wind is decelerated by diffusing interstellar cosmic rates, it is shown that the natural state of the termination shock is a gradual deceleration and compression, followed by a discontinuous jump to a downstream state which is dominated by the pressure contribution of the cosmic rays. A representative model is calculated for the steady state which incorporates both interstellar cosmic ray mediation and diffusively accelerated anomalous ions through a proposed thermal leakage mechanism. The interaction of large-scale disturbances with the equilibrium termination shock model is shown to result in some unusual downstream structure, including transmitted shocks and cosmic-ray-modified contact discontinuities. The structure observed may be connected to the 2-kHz outer heliospheric radio emission (Cairns et al., 1992a, b). The time-dependent simulations also demonstrate that interaction with solar wind compressible turbulence (e.g., traveling interplanetary shocks, etc.) could induce the termination shock to continually fluctuate between cosmic-ray-dominated and gas-dynamic states. This fluctuation may represent a partial explanation of the galactic cosmic ray modulation effect and illustrates that the Pioneer and Voyager satellites will encounter an evolving shock whose structure and dynamic properties are strongly influence by the mediation of interstellar and anomalous cosmic rays.

Steady state and dynamical structure of a cosmic-ray-modified termination shock

NASA Astrophysics Data System (ADS)

Donohue, D. J.; Zank, G. P.

1993-11-01

A hydrodynamic model is developed for the structure of a cosmic-ray-modified termination shock. The model is based on the two-fluid equations of diffuse shock acceleration (Drury and Volk, 1981). Both the steady state structure of the shock and its interaction with outer heliospheric disturbances are considered. Under the assumption that the solar wind is decelerated by diffusing interstellar cosmic rates, it is shown that the natural state of the termination shock is a gradual deceleration and compression, followed by a discontinuous jump to a downstream state which is dominated by the pressure contribution of the cosmic rays. A representative model is calculated for the steady state which incorporates both interstellar cosmic ray mediation and diffusively accelerated anomalous ions through a proposed thermal leakage mechanism. The interaction of large-scale disturbances with the equilibrium termination shock model is shown to result in some unusual downstream structure, including transmitted shocks and cosmic-ray-modified contact discontinuities. The structure observed may be connected to the 2-kHz outer heliospheric radio emission (Cairns et al., 1992a, b). The time-dependent simulations also demonstrate that interaction with solar wind compressible turbulence (e.g., traveling interplanetary shocks, etc.) could induce the termination shock to continually fluctuate between cosmic-ray-dominated and gas-dynamic states. This fluctuation may represent a partial explanation of the galactic cosmic ray modulation effect and illustrates that the Pioneer and Voyager satellites will encounter an evolving shock whose structure and dynamic properties are strongly influence by the mediation of interstellar and anomalous cosmic rays.

Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System's Dynamics: The Life Cycle of the Insulin Receptor.

PubMed

Scheidel, Jennifer; Lindauer, Klaus; Ackermann, Jörg; Koch, Ina

2015-12-17

The insulin-dependent activation and recycling of the insulin receptor play an essential role in the regulation of the energy metabolism, leading to a special interest for pharmaceutical applications. Thus, the recycling of the insulin receptor has been intensively investigated, experimentally as well as theoretically. We developed a time-resolved, discrete model to describe stochastic dynamics and study the approximation of non-linear dynamics in the context of timed Petri nets. Additionally, using a graph-theoretical approach, we analyzed the structure of the regulatory system and demonstrated the close interrelation of structural network properties with the kinetic behavior. The transition invariants decomposed the model into overlapping subnetworks of various sizes, which represent basic functional modules. Moreover, we computed the quasi-steady states of these subnetworks and demonstrated that they are fundamental to understand the dynamic behavior of the system. The Petri net approach confirms the experimental results of insulin-stimulated degradation of the insulin receptor, which represents a common feature of insulin-resistant, hyperinsulinaemic states.

Christopher Chang | NREL

Science.gov Websites

transition metal systems, macromolecular dynamics, comparative chemical bonding analysis, electron transfer . Research Interests Dynamics and control on discrete structures, including excited-state transition metal

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

PubMed Central

Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie D.

2010-01-01

Summary Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations utilizing experimental NMR and small-angle x-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. PMID:20399186

The architecture of dynamic reservoir in the echo state network

NASA Astrophysics Data System (ADS)

Cui, Hongyan; Liu, Xiang; Li, Lixiang

2012-09-01

Echo state network (ESN) has recently attracted increasing interests because of its superior capability in modeling nonlinear dynamic systems. In the conventional echo state network model, its dynamic reservoir (DR) has a random and sparse topology, which is far from the real biological neural networks from both structural and functional perspectives. We hereby propose three novel types of echo state networks with new dynamic reservoir topologies based on complex network theory, i.e., with a small-world topology, a scale-free topology, and a mixture of small-world and scale-free topologies, respectively. We then analyze the relationship between the dynamic reservoir structure and its prediction capability. We utilize two commonly used time series to evaluate the prediction performance of the three proposed echo state networks and compare them to the conventional model. We also use independent and identically distributed time series to analyze the short-term memory and prediction precision of these echo state networks. Furthermore, we study the ratio of scale-free topology and the small-world topology in the mixed-topology network, and examine its influence on the performance of the echo state networks. Our simulation results show that the proposed echo state network models have better prediction capabilities, a wider spectral radius, but retain almost the same short-term memory capacity as compared to the conventional echo state network model. We also find that the smaller the ratio of the scale-free topology over the small-world topology, the better the memory capacities.

Dynamic control of spin states in interacting magnetic elements

DOEpatents

Jain, Shikha; Novosad, Valentyn

2014-10-07

A method for the control of the magnetic states of interacting magnetic elements comprising providing a magnetic structure with a plurality of interacting magnetic elements. The magnetic structure comprises a plurality of magnetic states based on the state of each interacting magnetic element. The desired magnetic state of the magnetic structure is determined. The active resonance frequency and amplitude curve of the desired magnetic state is determined. Each magnetic element of the magnetic structure is then subjected to an alternating magnetic field or electrical current having a frequency and amplitude below the active resonance frequency and amplitude curve of said desired magnetic state and above the active resonance frequency and amplitude curve of the current state of the magnetic structure until the magnetic state of the magnetic structure is at the desired magnetic state.

Two Argonne scientists named 2012 AAAS fellows | Argonne National

Science.gov Websites

"contributions to understanding structural dynamics of molecular excited states with special . "I'm really interested in how molecules respond to light and how light could influence molecular is being honored for her "contributions to understanding structural dynamics of molecular

Mapping hydration dynamics around a protein surface

PubMed Central

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2007-01-01

Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few (≈1–8 ps) and tens to hundreds of picoseconds (≈20–200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water–protein interactions fluctuate on picosecond time scales. PMID:18003912

Relation between native ensembles and experimental structures of proteins

PubMed Central

Best, Robert B.; Lindorff-Larsen, Kresten; DePristo, Mark A.; Vendruscolo, Michele

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of “high-sequence similarity Protein Data Bank” (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble. PMID:16829580

Elucidating Peptide and Protein Structure and Dynamics: UV Resonance Raman Spectroscopy

PubMed Central

Oladepo, Sulayman A.; Xiong, Kan; Hong, Zhenmin; Asher, Sanford A.

2011-01-01

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III3 band and the Cα-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 310- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures. PMID:21379371

Principles underlying the Fourth Power Nature of Structured Shock Waves

NASA Astrophysics Data System (ADS)

Grady, Dennis

2017-06-01

Steady structured shock waves in materials including metals, glasses, compounds and solid mixtures, when represented through plots of Hugoniot stress against a measure of the strain rate through which the Hugoniot state is achieved, have consistently demonstrated a dependence to the fourth power. A perhaps deeper observation is that the product of the energy dissipated through the transition to the Hugoniot state and the time duration of the Hugoniot state event exhibits invariance independent of the Hugoniot amplitude. Invariance of the energy-time product and the fourth-power trend are to first order equivalent. Further, constancy of this energy-time product is observed in other dynamic critical state failure events including spall fracture, dynamic compaction and adiabatic shear failure. The presentation pursues the necessary background exposing the foregoing shock physics observations and explores possible statistical physics principals that may underlie the collective dynamic observations.

Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c.

PubMed

Imai, Mizue; Saio, Tomohide; Kumeta, Hiroyuki; Uchida, Takeshi; Inagaki, Fuyuhiko; Ishimori, Koichiro

2016-01-22

Redox-dependent changes in the structure and dynamics of human cytochrome c (Cyt c) were investigated by solution NMR. We found significant structural changes in several regions, including residues 23-28 (loop 3), which were further corroborated by chemical shift differences between the reduced and oxidized states of Cyt c. These differences are essential for discriminating redox states in Cyt c by cytochrome c oxidase (CcO) during electron transfer reactions. Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments identified that the region around His33 undergoes conformational exchanges on the μs-ms timescale, indicating significant redox-dependent structural changes. Because His33 is not part of the interaction site for CcO, our data suggest that the dynamic properties of the region, which is far from the interaction site for CcO, contribute to conformational changes during electron transfer to CcO. Copyright © 2015 Elsevier Inc. All rights reserved.

The effects of disulfide bonds on the denatured state of barnase.

PubMed Central

Clarke, J.; Hounslow, A. M.; Bond, C. J.; Fersht, A. R.; Daggett, V.

2000-01-01

The effects of engineered disulfide bonds on protein stability are poorly understood because they can influence the structure, dynamics, and energetics of both the native and denatured states. To explore the effects of two engineered disulfide bonds on the stability of barnase, we have conducted a combined molecular dynamics and NMR study of the denatured state of the two mutants. As expected, the disulfide bonds constrain the denatured state. However, specific extended beta-sheet structure can also be detected in one of the mutant proteins. This mutant is also more stable than would be predicted. Our study suggests a possible cause of the very high stability conferred by this disulfide bond: the wild-type denatured ensemble is stabilized by a nonnative hydrophobic cluster, which is constrained from occurring in the mutant due to the formation of secondary structure. PMID:11206061

Surface hopping investigation of the relaxation dynamics in radical cations

DOE PAGES

Assmann, Mariana; Weinacht, Thomas; Matsika, Spiridoula

2016-01-19

Ionization processes can lead to the formation of radical cations with population in several ionic states. In this study, we examine the dynamics of three radical cations starting from an excited ionic state using trajectory surface hopping dynamics in combination with multiconfigurational electronic structure methods. The efficiency of relaxation to the ground state is examined in an effort to understand better whether fragmentation of cations is likely to occur directly on excited states or after relaxation to the ground state. The results on cyclohexadiene, hexatriene, and uracil indicate that relaxation to the ground ionic state is very fast in thesemore » systems, while fragmentation before relaxation is rare. Ultrafast relaxation is facilitated by the close proximity of electronic states and the presence of two- and three-state conical intersections. Furthermore, examining the properties of the systems in the Franck-Condon region can give some insight into the subsequent dynamics.« less

Dynamic Folding Pathway Models of the Trp-Cage Protein

PubMed Central

Kim, Seung-Yeon

2013-01-01

Using action-derived molecular dynamics (ADMD), we study the dynamic folding pathway models of the Trp-cage protein by providing its sequential conformational changes from its initial disordered structure to the final native structure at atomic details. We find that the numbers of native contacts and native hydrogen bonds are highly correlated, implying that the native structure of Trp-cage is achieved through the concurrent formations of native contacts and native hydrogen bonds. In early stage, an unfolded state appears with partially formed native contacts (~40%) and native hydrogen bonds (~30%). Afterward, the folding is initiated by the contact of the side chain of Tyr3 with that of Trp6, together with the formation of the N-terminal α-helix. Then, the C-terminal polyproline structure docks onto the Trp6 and Tyr3 rings, resulting in the formations of the hydrophobic core of Trp-cage and its near-native state. Finally, the slow adjustment processes of the near-native states into the native structure are dominant in later stage. The ADMD results are in agreement with those of the experimental folding studies on Trp-cage and consistent with most of other computational studies. PMID:23865078

Brain dynamics of post-task resting state are influenced by expertise: Insights from baseball players.

PubMed

Muraskin, Jordan; Dodhia, Sonam; Lieberman, Gregory; Garcia, Javier O; Verstynen, Timothy; Vettel, Jean M; Sherwin, Jason; Sajda, Paul

2016-12-01

Post-task resting state dynamics can be viewed as a task-driven state where behavioral performance is improved through endogenous, non-explicit learning. Tasks that have intrinsic value for individuals are hypothesized to produce post-task resting state dynamics that promote learning. We measured simultaneous fMRI/EEG and DTI in Division-1 collegiate baseball players and compared to a group of controls, examining differences in both functional and structural connectivity. Participants performed a surrogate baseball pitch Go/No-Go task before a resting state scan, and we compared post-task resting state connectivity using a seed-based analysis from the supplementary motor area (SMA), an area whose activity discriminated players and controls in our previous results using this task. Although both groups were equally trained on the task, the experts showed differential activity in their post-task resting state consistent with motor learning. Specifically, we found (1) differences in bilateral SMA-L Insula functional connectivity between experts and controls that may reflect group differences in motor learning, (2) differences in BOLD-alpha oscillation correlations between groups suggests variability in modulatory attention in the post-task state, and (3) group differences between BOLD-beta oscillations that may indicate cognitive processing of motor inhibition. Structural connectivity analysis identified group differences in portions of the functionally derived network, suggesting that functional differences may also partially arise from variability in the underlying white matter pathways. Generally, we find that brain dynamics in the post-task resting state differ as a function of subject expertise and potentially result from differences in both functional and structural connectivity. Hum Brain Mapp 37:4454-4471, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation

PubMed Central

2017-01-01

The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability. PMID:29186132

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

PubMed Central

Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

2016-01-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts. PMID:27124275

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

PubMed

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Dynamic structural states of ClpB involved in its disaggregation function.

PubMed

Uchihashi, Takayuki; Watanabe, Yo-Hei; Nakazaki, Yosuke; Yamasaki, Takashi; Watanabe, Hiroki; Maruno, Takahiro; Ishii, Kentaro; Uchiyama, Susumu; Song, Chihong; Murata, Kazuyoshi; Iino, Ryota; Ando, Toshio

2018-06-01

The ATP-dependent bacterial protein disaggregation machine, ClpB belonging to the AAA+ superfamily, refolds toxic protein aggregates into the native state in cooperation with the cognate Hsp70 partner. The ring-shaped hexamers of ClpB unfold and thread its protein substrate through the central pore. However, their function-related structural dynamics has remained elusive. Here we directly visualize ClpB using high-speed atomic force microscopy (HS-AFM) to gain a mechanistic insight into its disaggregation function. The HS-AFM movies demonstrate massive conformational changes of the hexameric ring during ATP hydrolysis, from a round ring to a spiral and even to a pair of twisted half-spirals. HS-AFM observations of Walker-motif mutants unveil crucial roles of ATP binding and hydrolysis in the oligomer formation and structural dynamics. Furthermore, repressed and hyperactive mutations result in significantly different oligomeric forms. These results provide a comprehensive view for the ATP-driven oligomeric-state transitions that enable ClpB to disentangle protein aggregates.

Dynamic loading and stress life analysis of permanent space station modules

NASA Astrophysics Data System (ADS)

Anisimov, A. V.; Krokhin, I. A.; Likhoded, A. I.; Malinin, A. A.; Panichkin, N. G.; Sidorov, V. V.; Titov, V. A.

2016-11-01

Some methodological approaches to solving several key problems of dynamic loading and structural strength analysis of Permanent Space Station (PSS)modules developed on the basis of the working experience of Soviet and Russian PSS and the International Space station (ISS) are presented. The solutions of the direct and semi-inverse problems of PSS structure dynamics are mathematically stated. Special attention is paid to the use of the results of ground structural strength tests of space station modules and the data on the actual flight actions on the station and its dynamic responses in the orbital operation regime. The procedure of determining the dynamics and operation life parameters of elements of the PSS modules is described.

Solitary waves and nonlinear dynamic coherent structures in magnetic metamaterials

NASA Astrophysics Data System (ADS)

Tankeyev, A. P.; Smagin, V. V.; Borich, M. A.; Zhuravlev, A. S.

2009-03-01

Within the framework of the extended nonlinear Schrödinger equation (ENSE), two types of nonlinear states of magnetization in a ferromagnet-dielectric-metal metamagnetic structure have been obtained and investigated. These states have an internal structure; e.g., a periodic sequence of compound solitons is formed by kink-antikink pairs (shock waves), and coherent periodic breather structures are formed by “bright” quasi-solitons. Conditions have been found under which the envelope of these states is described by a modified Korteweg-de Vries (mKdV) equation. It is shown that the compound solitons are described by an mKdV equation with repulsion, and the breather structures, by an mKdV equation with attraction. It is shown also that the characteristic properties of the solutions are determined by the sign of the group-velocity dispersion rather than by the sign of the group velocity itself. The results obtained can be used for searching new nonlinear dynamic coherent structures, e.g., compound solitons and breathers in high-dispersion magnetic metamaterials.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00980a Click here for additional data file.

PubMed Central

Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E.

2017-01-01

γ-Secretase is an intramembrane-cleaving aspartyl protease that plays an essential role in the processing of a variety of integral membrane proteins. Its role in the ultimate cleavage step in the processing of amyloid precursor protein to form amyloid-β (Aβ) peptide makes it an important therapeutic target in Alzheimer's disease research. Significant recent advances have been made in structural studies of this critical membrane protein complex. However, details of the mechanism of activation of the enzyme complex remain unclear. Using a multiscale computational modeling approach, combining multiple coarse-grained microsecond dynamic trajectories with all-atom models, the structure and two conformational states of the γ-secretase complex were evaluated. The transition between enzymatic state 1 and state 2 is shown to critically depend on the protonation states of the key catalytic residues Asp257 and Asp385 in the active site domain. The active site formation, related to our γ-secretase state 2, is observed to involve a concerted movement of four transmembrane helices from the catalytic subunit, resulting in the required localization of the catalytic residues. Global analysis of the structural ensemble of the enzyme complex was used to identify collective fluctuations important to the mechanism of substrate recognition and demonstrate that the corresponding fluctuations observed were uncorrelated with structural changes associated with enzyme activation. Overall, this computational study provides essential insight into the role of structure and dynamics in the activation and function of γ-secretase. PMID:28970936

Nonlinear dynamics and damage induced properties of soft matter with application in oncology

NASA Astrophysics Data System (ADS)

Naimark, O.

2017-09-01

Molecular-morphological signs of oncogenesis could be linked to multiscale collective effects in molecular, cell and tissue related to defects (damage) dynamics. It was shown that nonlinear behavior of biological systems can be linked to the existence of characteristic collective open state modes providing the coherent expression dynamics. New type of criticality in nonequilibrium systems with defects—structural-scaling transition allows the definition of the `driving force' for a biological soft matter related to consolidated open states. The set of collective open states (breathers, autosolitons and blow-up modes) in the molecular ensembles provides the collective expression dynamics to attract the entire system (cell, tissue) toward a few preferred global states. The co-existence of three types of collective modes determines the multifractal scenario of biological soft matter dynamics. The appearance of `globally convergent' dynamics corresponding to the coherent behavior of multiscale blow-up open states (blow-up gene expression) leads to anomalous localized softening (blow-up localized damage) and the subjection of the cells (or tissue) to monofractal dynamics. This dynamics can be associated with cancer progression.

Learning to generate combinatorial action sequences utilizing the initial sensitivity of deterministic dynamical systems.

PubMed

Nishimoto, Ryu; Tani, Jun

2004-09-01

This study shows how sensory-action sequences of imitating finite state machines (FSMs) can be learned by utilizing the deterministic dynamics of recurrent neural networks (RNNs). Our experiments indicated that each possible combinatorial sequence can be recalled by specifying its respective initial state value and also that fractal structures appear in this initial state mapping after the learning converges. We also observed that the sequences of mimicking FSMs are encoded utilizing the transient regions rather than the invariant sets of the evolved dynamical systems of the RNNs.

Harmonic Brain Modes: A Unifying Framework for Linking Space and Time in Brain Dynamics.

PubMed

Atasoy, Selen; Deco, Gustavo; Kringelbach, Morten L; Pearson, Joel

2018-06-01

A fundamental characteristic of spontaneous brain activity is coherent oscillations covering a wide range of frequencies. Interestingly, these temporal oscillations are highly correlated among spatially distributed cortical areas forming structured correlation patterns known as the resting state networks, although the brain is never truly at "rest." Here, we introduce the concept of harmonic brain modes-fundamental building blocks of complex spatiotemporal patterns of neural activity. We define these elementary harmonic brain modes as harmonic modes of structural connectivity; that is, connectome harmonics, yielding fully synchronous neural activity patterns with different frequency oscillations emerging on and constrained by the particular structure of the brain. Hence, this particular definition implicitly links the hitherto poorly understood dimensions of space and time in brain dynamics and its underlying anatomy. Further we show how harmonic brain modes can explain the relationship between neurophysiological, temporal, and network-level changes in the brain across different mental states ( wakefulness, sleep, anesthesia, psychedelic). Notably, when decoded as activation of connectome harmonics, spatial and temporal characteristics of neural activity naturally emerge from the interplay between excitation and inhibition and this critical relation fits the spatial, temporal, and neurophysiological changes associated with different mental states. Thus, the introduced framework of harmonic brain modes not only establishes a relation between the spatial structure of correlation patterns and temporal oscillations (linking space and time in brain dynamics), but also enables a new dimension of tools for understanding fundamental principles underlying brain dynamics in different states of consciousness.

Excited State Structural Dynamics of Carotenoids and ChargeTransfer Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Tassle, Aaron Justin

This dissertation describes the development andimplementation of a visible/near infrared pump/mid-infrared probeapparatus. Chapter 1 describes the background and motivation ofinvestigating optically induced structural dynamics, paying specificattention to solvation and the excitation selection rules of highlysymmetric molecules such as carotenoids. Chapter 2 describes thedevelopment and construction of the experimental apparatus usedthroughout the remainder of this dissertation. Chapter 3 will discuss theinvestigation of DCM, a laser dye with a fluorescence signal resultingfrom a charge transfer state. By studying the dynamics of DCM and of itsmethyl deuterated isotopomer (an otherwise identical molecule), we areable to investigate the origins of the charge transfer statemore » and provideevidence that it is of the controversial twisted intramolecular (TICT)type. Chapter 4 introduces the use of two-photon excitation to the S1state, combined with one-photon excitation to the S2 state of thecarotenoid beta-apo-8'-carotenal. These 2 investigations show evidencefor the formation of solitons, previously unobserved in molecular systemsand found only in conducting polymers Chapter 5 presents an investigationof the excited state dynamics of peridinin, the carotenoid responsiblefor the light harvesting of dinoflagellates. This investigation allowsfor a more detailed understanding of the importance of structuraldynamics of carotenoids in light harvesting.« less

Structural and dynamical properties of recombining ultracold neutral plasma

NASA Astrophysics Data System (ADS)

Tiwari, Sanat Kumar; Shaffer, Nathaniel R.; Baalrud, Scott D.

2017-10-01

An ultracold plasma (UCP) is an evolving collection of free charges and bound charges (Rydberg atoms). Over time, bound species concentration increases due to recombination. We present the structural and dynamical properties of an evolving UCP using classical molecular dynamics simulation. Coulomb collapse is avoided using a repulsive core with the attractive Coulomb potential. The repulsive core size controls the concentration of bound states, as it determines the depth of the potential well between opposite charges. We vary the repulsive core size to emulate the quasi-static state of plasma at different time during the evolution. Binary, chain and ring-like bound states are observed in the simulation carried out at different coupling strengths and repulsive core size. The effect of bound states can be seen as molecular peaks in the radial distribution function (RDF). The thermodynamic properties associated with the free charges can be analyzed from RDF by separating free from bound states. These bound states also change the dynamical properties of the plasma. The electron velocity auto-correlation displays oscillations due to the orbital motion in bound states. These bound states act like a neutral species, damping electron plasmon modes and broadening the ion acoustic mode. This work is supported by AFOSR Grant Number FA9550-16-1-0221. It used computational resources by XSEDE, which is supported by NSF Grant Number ACI-1053575.

Atomic-level characterization of the structural dynamics of proteins.

PubMed

Shaw, David E; Maragakis, Paul; Lindorff-Larsen, Kresten; Piana, Stefano; Dror, Ron O; Eastwood, Michael P; Bank, Joseph A; Jumper, John M; Salmon, John K; Shan, Yibing; Wriggers, Willy

2010-10-15

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.

Model of photoinduced structural change induced by THz pulse irradiation

NASA Astrophysics Data System (ADS)

Ishida, Kunio; Nasu, Keiichiro

Recently intense optical pulses with THz frequency have been obtained, and it is of interest to study the effect of irradiated THz pulses on electronic systems. We theoretically study the photoinduced cooperative dynamics triggered by irradiation of THz pulses. We employed a model of two-level localized electrons coupled with an optical phonon mode taking into account the nonadiabaticity of the electron dynamics, and solved the time-dependent Schrödinger equation numerically. We consider the cases in which the THz pulses create phonons near the surface of the system, and pursue the electronic transitions induced by the propagation of the phonons. We found that they are able to induce excited-state domain growth, and that the interference between them plays an important role in the growth dynamics. Hence, the domain growth is affected by the geometry of the surface of the system, which is different from the photoinduced structural change by visible/UV pulses. We also show that the nonadiabatic/adiabatic electronic transitions should be taken into account though the domain growth mainly proceeds on the ground-state potential energy surfaces(PESs). In other words, the energy level/structure of excited-state PESs are relevant to the domain-growth dynamics.

Dynamical spin structure factors of α-RuCl3

NASA Astrophysics Data System (ADS)

Suzuki, Takafumi; Suga, Sei-ichiro

2018-03-01

Honeycomb-lattice magnet α-RuCl3 is considered to be a potential candidate of realizing Kitaev spin liquid, although this material undergoes a phase transition to the zigzag magnetically ordered state at T N ∼ 7 K. Quite recently, inelastic neutron-scattering experiments using single crystal α-RuCl3 have unveiled characteristic dynamical properties. We calculate dynamical spin structure factors of three ab-initio models for α-RuCl3 with an exact numerical diagonalization method. We also calculate temperature dependences of the specific heat by employing thermal pure quantum states. We compare our numerical results with the experiments and discuss characteristics obtained by using three ab-initio models.

Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowers, Geoffrey

United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).

Sliding mode control based on Kalman filter dynamic estimation of battery SOC

NASA Astrophysics Data System (ADS)

He, Dongmeia; Hou, Enguang; Qiao, Xin; Liu, Guangmin

2018-06-01

Lithium-ion battery charge state of the accurate and rapid estimation of battery management system is the key technology. In this paper, an exponentially reaching law sliding-mode variable structure control algorithm based on Kalman filter is proposed to estimate the state of charge of Li-ion battery for the dynamic nonlinear system. The RC equivalent circuit model is established, and the model equation with specific structure is given. The proposed Kalman filter sliding mode structure is used to estimate the state of charge of the battery in the battery model, and the jitter effect can be avoided and the estimation performance can be improved. The simulation results show that the proposed Kalman filter sliding mode control has good accuracy in estimating the state of charge of the battery compared with the ordinary Kalman filter, and the error range is within 3%.

Partial dynamical symmetry and the vibrational structure of Cd isotopes

NASA Astrophysics Data System (ADS)

Leviatan, A.; Gavrielov, N.; García-Ramos, J. E.; Van Isacker, P.

2018-05-01

The recently reported deviations of selected non-yrast states in 110Cd from the expected sphericalvibrator behaviour, is addressed by means of an Hamiltonian with U(5) partial dynamical symmetry. The latter preserves the U(5) symmetry in a segment of the spectrum and breaks it in other states. The effect of intruder states is treated in the framework of the interacting boson model with configuration mixing.

Probing the solvation structure and dynamics in ionic liquids by time-resolved infrared spectroscopy of 4-(dimethylamino)benzonitrile.

PubMed

Ando, Rômulo A; Brown-Xu, Samantha E; Nguyen, Lisa N Q; Gustafson, Terry L

2017-09-20

In this work we demonstrate the use of the push-pull model system 4-(dimethylamino)benzonitrile (DMABN) as a convenient molecular probe to investigate the local solvation structure and dynamics by means of time-resolved infrared spectroscopy (TRIR). The photochemical features associated with this system provide several advantages due to the high charge separation between the ground and charge transfer states involving the characteristic nitrile bond, and an excited state lifetime that is long enough to observe the slow solvation dynamics in organic solvents and ionic liquids. The conversion from a locally excited state to an intramolecular charge transfer state (LE-ICT) in ionic liquids shows similar kinetic lifetimes in comparison to organic solvents. This similarity confirms that such conversion depends solely on the intramolecular reorganization of DMABN in the excited state, and not by the dynamics of solvation. In contrast, the relative shift of the ν(CN) vibration during the relaxation of the ICT state reveals two distinct lifetimes that are sensitive to the solvent environment. This study reveals a fast time component which is attributed to the dipolar relaxation of the solvent and a slower time component related to the rotation of the dimethylamino group of DMABN.

Classification of Dynamical Diffusion States in Single Molecule Tracking Microscopy

PubMed Central

Bosch, Peter J.; Kanger, Johannes S.; Subramaniam, Vinod

2014-01-01

Single molecule tracking of membrane proteins by fluorescence microscopy is a promising method to investigate dynamic processes in live cells. Translating the trajectories of proteins to biological implications, such as protein interactions, requires the classification of protein motion within the trajectories. Spatial information of protein motion may reveal where the protein interacts with cellular structures, because binding of proteins to such structures often alters their diffusion speed. For dynamic diffusion systems, we provide an analytical framework to determine in which diffusion state a molecule is residing during the course of its trajectory. We compare different methods for the quantification of motion to utilize this framework for the classification of two diffusion states (two populations with different diffusion speed). We found that a gyration quantification method and a Bayesian statistics-based method are the most accurate in diffusion-state classification for realistic experimentally obtained datasets, of which the gyration method is much less computationally demanding. After classification of the diffusion, the lifetime of the states can be determined, and images of the diffusion states can be reconstructed at high resolution. Simulations validate these applications. We apply the classification and its applications to experimental data to demonstrate the potential of this approach to obtain further insights into the dynamics of cell membrane proteins. PMID:25099798

Spectroscopy of Isolated Prebiotic Nucleobases

NASA Technical Reports Server (NTRS)

Svadlenak, Nathan; Callahan, Michael P.; Ligare, Marshall; Gulian, Lisa; Gengeliczki, Zsolt; Nachtigallova, Dana; Hobza, Pavel; deVries, Mattanjah

2011-01-01

We use multiphoton ionization and double resonance spectroscopy to study the excited state dynamics of biologically relevant molecules as well as prebiotic nucleobases, isolated in the gas phase. Molecules that are biologically relevant to life today tend to exhibit short excited state lifetimes compared to similar but non-biologically relevant analogs. The mechanism is internal conversion, which may help protect the biologically active molecules from UV damage. This process is governed by conical intersections that depend very strongly on molecular structure. Therefore we have studied purines and pyrimidines with systematic variations of structure, including substitutions, tautomeric forms, and cluster structures that represent different base pair binding motifs. These structural variations also include possible alternate base pairs that may shed light on prebiotic chemistry. With this in mind we have begun to probe the ultrafast dynamics of molecules that exhibit very short excited states and search for evidence of internal conversions.

Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level.

PubMed

Fleig, Timo; Knecht, Stefan; Hättig, Christof

2007-06-28

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

Exploring the Influence of Dynamic Disorder on Excitons in Solid Pentacene

NASA Astrophysics Data System (ADS)

Wang, Zhiping; Sharifzadeh, Sahar; Doak, Peter; Lu, Zhenfei; Neaton, Jeffrey

2014-03-01

A complete understanding of the spectroscopic and charge transport properties of organic semiconductors requires knowledge of the role of thermal fluctuations and dynamic disorder. We present a first-principles theoretical study aimed at understanding the degree to which dynamic disorder at room temperature results in energy level broadening and excited-state localization within bulk crystalline pentacene. Ab initio molecular dynamics simulations are well-equilibrated for 7-9 ps and tens of thousands of structural snapshots, taken at 0.5 fs intervals, provide input for many-body perturbation theory within the GW approximation and Bethe-Salpeter equation (BSE) approach. The GW-corrected density of states, including thousands of snapshots, indicates that thermal fluctuations significantly broaden the valence and conduction states by >0.2 eV. Additionally, we investigate the nature and energy of the lowest energy singlet and triplet excitons, computed for a set of uncorrelated and energetically preferred structures. This work supported by DOE; computational resources provided by NERSC.

Lattice dynamics, elasticity and magnetic abnormality in ordered crystalline alloys Fe3Pt at high pressures

NASA Astrophysics Data System (ADS)

Cheng, Tai-min; Yu, Guo-Liang; Su, Yong; Ge, Chong-Yuan; Zhang, Xin-Xin; Zhu, Lin; Li, Lin

2018-05-01

The ordered crystalline Invar alloy Fe3Pt is in a special magnetic critical state, under which the lattice dynamic stability of the system is extremely sensitive to external pressures. We studied the pressure dependence of enthalpy and magnetism of Fe3Pt in different crystalline alloys by using the first-principles projector augmented-wave method based on the density functional theory. Results show that the P4/mbm structure is the ground state structure and is more stable relative to other structures at pressures below 18.54 GPa. The total magnetic moments of L12, I4/mmm and DO22 structures decrease rapidly with pressure and oscillate near the ferromagnetic collapse critical pressure. At the pressure of 43 GPa, the ferrimagnetic property in DO22 structure becomes apparently strengthened and its volume increases rapidly. The lattice dynamics calculation for L12 structures at high pressures shows that the spontaneous magnetization of the system in ferromagnetic states induces the softening of the transverse acoustic phonon TA1 (M), and there exists a strong spontaneous volume magnetostriction at pressures below 26.95 GPa. Especially, the lattice dynamics stability is sensitive to pressure, in the pressure range between the ferromagnetic collapse critical pressure (41.9 GPa) and the magnetism completely disappearing pressure (57.25 GPa), and near the pressure of phase transition from L12 to P4/mbm structure (27.27 GPa). Moreover, the instability of magnetic structure leads to a prominent elastic modulus oscillation, and the spin polarizability of electrons near the Fermi level is very sensitive to pressures in that the pressure range. The pressure induces the stability of the phonon spectra of the system at pressures above 57.25 GPa.

Quantum molecular dynamics study on the structures and dc conductivity of warm dense silane

NASA Astrophysics Data System (ADS)

Sun, Huayang; Kang, Dongdong; Dai, Jiayu; Zeng, Jiaolong; Yuan, Jianmin

2014-02-01

The ionic and electronic structures of warm dense silane at the densities of 1.795, 2.260, 3.382, and 3.844 g/cm3 have been studied with temperatures from 1000 K to 3 eV using quantum molecular dynamics simulations. At all densities, the structures are melted above 1000 K. The matter states are characterized as polymeric from 1000 to 4000 K and become dense plasma states with further increasing temperature to 1 eV. At two lower densities of 1.795 and 2.260 g/cm3, silane first dissociates and then becomes the polymeric state via a chain state from the initial crystalline structure. At higher densities, however, no dissociation stage was found. These findings can help us understand how the warm dense matter forms. A rise is found for the direct current electric conductivity at T ˜1000 K, indicating the nonmetal-to-metal transition. The conductivity decreases slightly with the increase of temperature, which is due to the more disordered structures at higher temperatures.

Rating of Dynamic Coefficient for Simple Beam Bridge Design on High-Speed Railways

NASA Astrophysics Data System (ADS)

Diachenko, Leonid; Benin, Andrey; Smirnov, Vladimir; Diachenko, Anastasia

2018-06-01

The aim of the work is to improve the methodology for the dynamic computation of simple beam spans during the impact of high-speed trains. Mathematical simulation utilizing numerical and analytical methods of structural mechanics is used in the research. The article analyses parameters of the effect of high-speed trains on simple beam spanning bridge structures and suggests a technique of determining of the dynamic index to the live load. Reliability of the proposed methodology is confirmed by results of numerical simulation of high-speed train passage over spans with different speeds. The proposed algorithm of dynamic computation is based on a connection between maximum acceleration of the span in the resonance mode of vibrations and the main factors of stress-strain state. The methodology allows determining maximum and also minimum values of the main efforts in the construction that makes possible to perform endurance tests. It is noted that dynamic additions for the components of the stress-strain state (bending moments, transverse force and vertical deflections) are different. This condition determines the necessity for differentiated approach to evaluation of dynamic coefficients performing design verification of I and II groups of limiting state. The practical importance: the methodology of determining the dynamic coefficients allows making dynamic calculation and determining the main efforts in split beam spans without numerical simulation and direct dynamic analysis that significantly reduces the labour costs for design.

Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR

PubMed Central

Camilloni, Carlo; Schaal, Daniel; Schweimer, Kristian; Schwarzinger, Stephan; De Simone, Alfonso

2012-01-01

The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides. In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a group of neurodegenerative disorders known as transmissible spongiform encephalopathies. Our combined approach allowed us to dissect the factors that govern the conformational states of PrP-H1 in solution, and the implications of these factors for prion protein misfolding and aggregation. The results underline the importance of adopting novel integrated approaches that take advantage of experiments and theory to achieve a comprehensive characterization of the structure and dynamics of biological macromolecules. PMID:22225810

Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.

PubMed

Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Shaw, David E

2016-01-01

Molecular dynamics (MD) simulation is a well-established tool for the computational study of protein structure and dynamics, but its application to the important problem of protein structure prediction remains challenging, in part because extremely long timescales can be required to reach the native structure. Here, we examine the extent to which the use of low-resolution information in the form of residue-residue contacts, which can often be inferred from bioinformatics or experimental studies, can accelerate the determination of protein structure in simulation. We incorporated sets of 62, 31, or 15 contact-based restraints in MD simulations of ubiquitin, a benchmark system known to fold to the native state on the millisecond timescale in unrestrained simulations. One-third of the restrained simulations folded to the native state within a few tens of microseconds-a speedup of over an order of magnitude compared with unrestrained simulations and a demonstration of the potential for limited amounts of structural information to accelerate structure determination. Almost all of the remaining ubiquitin simulations reached near-native conformations within a few tens of microseconds, but remained trapped there, apparently due to the restraints. We discuss potential methodological improvements that would facilitate escape from these near-native traps and allow more simulations to quickly reach the native state. Finally, using a target from the Critical Assessment of protein Structure Prediction (CASP) experiment, we show that distance restraints can improve simulation accuracy: In our simulations, restraints stabilized the native state of the protein, enabling a reasonable structural model to be inferred. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

An ab initio study of the structure and dynamics of bulk liquid Ag and its liquid-vapor interface

NASA Astrophysics Data System (ADS)

Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique; Gonzalez Fernandez, David Jose

Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behaviour with two different wavelenghts, as the spacing between the outer and first inner layer is different from that between the other inner layers.

Signs of universality in the structure of culture

NASA Astrophysics Data System (ADS)

Băbeanu, Alexandru-Ionuţ; Talman, Leandros; Garlaschelli, Diego

2017-11-01

Understanding the dynamics of opinions, preferences and of culture as whole requires more use of empirical data than has been done so far. It is clear that an important role in driving this dynamics is played by social influence, which is the essential ingredient of many quantitative models. Such models require that all traits are fixed when specifying the "initial cultural state". Typically, this initial state is randomly generated, from a uniform distribution over the set of possible combinations of traits. However, recent work has shown that the outcome of social influence dynamics strongly depends on the nature of the initial state. If the latter is sampled from empirical data instead of being generated in a uniformly random way, a higher level of cultural diversity is found after long-term dynamics, for the same level of propensity towards collective behavior in the short-term. Moreover, if the initial state is randomized by shuffling the empirical traits among people, the level of long-term cultural diversity is in-between those obtained for the empirical and uniformly random counterparts. The current study repeats the analysis for multiple empirical data sets, showing that the results are remarkably similar, although the matrix of correlations between cultural variables clearly differs across data sets. This points towards robust structural properties inherent in empirical cultural states, possibly due to universal laws governing the dynamics of culture in the real world. The results also suggest that this dynamics might be characterized by criticality and involve mechanisms beyond social influence.

Mixed state dynamical quantum phase transitions

NASA Astrophysics Data System (ADS)

Bhattacharya, Utso; Bandyopadhyay, Souvik; Dutta, Amit

2017-11-01

Preparing an integrable system in a mixed state described by a thermal density matrix, we subject it to a sudden quench and explore the subsequent unitary dynamics. To address the question of whether the nonanalyticities, namely, the dynamical quantum phase transitions (DQPTs), persist when the initial state is mixed, we consider two versions of the generalized Loschmidt overlap amplitude (GLOA). Our study shows that the GLOA constructed using the Uhlmann approach does not show any signature of DQPTs at any nonzero initial temperature. On the other hand, a GLOA defined in the interferometric phase approach through the purifications of the time-evolved density matrix, indeed shows that nonanalyiticies in the corresponding "dynamical free-energy density" persist, thereby establishing the existence of mixed state dynamical quantum phase transitions (MSDQPTs). Our work provides a framework that perfectly reproduces both the nonanalyticities and also the emergent topological structure in the pure state limit. These claims are corroborated by analyzing the nonequilibrium dynamics of a transverse Ising chain initially prepared in a thermal state and subjected to a sudden quench of the transverse field.

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

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.

Catch and Release: Orbital Symmetry Guided Reaction Dynamics from a Freed “Tension Trapped Transition State”

DOE PAGES

Wang, Junpeng; Ong, Mitchell T.; Kouznetsova, Tatiana B.; ...

2015-08-31

The dynamics of reactions at or in the immediate vicinity of transition states are critical to reaction rates and product distributions, but direct experimental probes of those dynamics are rare. In this paper, s-trans, s-trans 1,3-diradicaloid transition states are trapped by tension along the backbone of purely cis-substituted gem-difluorocyclopropanated polybutadiene using the extensional forces generated by pulsed sonication of dilute polymer solutions. Once released, the branching ratio between symmetry-allowed disrotatory ring closing (of which the trapped diradicaloid structure is the transition state) and symmetry-forbidden conrotatory ring closing (whose transition state is nearby) can be inferred. Finally, net conrotatory ring closingmore » occurred in 5.0 ± 0.5% of the released transition states, in excellent agreement with ab initio molecular dynamics simulations.« less

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method

NASA Astrophysics Data System (ADS)

Miura, Shinichi

2018-03-01

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method.

PubMed

Miura, Shinichi

2018-03-14

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Ultrafast Excited-State Dynamics of Cytosine Aza-Derivative and Analogues.

PubMed

Zhou, Zhongneng; Zhou, Xueyao; Wang, Xueli; Jiang, Bin; Li, Yongle; Chen, Jinquan; Xu, Jianhua

2017-04-13

Excited state dynamics of 5-azacytosine (5-AC), 2,4-diamino-1,3,5-triazine (2,4-DT), and 2-amino-1,3,5-triazine (2-AT) were comprehensively investigated by steady state absorption, fluorescence, and femtosecond transient absorption measurements. Time-dependent density functional theory (TDDFT) calculations were performed to help assign the absorption bands and understand the excited state decay mechanisms. The experimental results of excited singlet state dynamics for 5-AC, 2,4-DT, and 2-AT with femtosecond time resolution were reported for the first time. Two distinct decay pathways, with ∼1 ps and tens of picosecond lifetimes, were observed in 5-AC. Only one decay pathway with 17 ps lifetime was observed in 2,4-DT while an emissive state was found in 2-AT. TDDFT calculations suggest that 5-AC has a dark nπ* (S 1 ) state below the first allowed ππ* (S 2 ) state, which leads to the ultrafast decay of the ππ* state. In 2,4-DT, there is no dark nπ* state below the bright ππ* (S 1 ) state and the 17 ps lifetime is assigned to the relaxation from the ππ* (S 1 ) state to ground state. Two dark nπ* states (S 1 and S 2 ) were found in 2-AT, which exhibits much more complex excited state dynamics compared with the other two. Photoluminescence in 2-AT has been confirmed to be fluorescence emission from its bright ππ* (S 3 ) state. Our results strongly suggest that electronic structures are very sensitive to the substitution on the triazine ring and that the photophysical properties of nucleic acid analogues depend highly on their molecular structures.

Bursting and critical layer frequencies in minimal turbulent dynamics and connections to exact coherent states

NASA Astrophysics Data System (ADS)

Park, Jae Sung; Shekar, Ashwin; Graham, Michael D.

2018-01-01

The dynamics of the turbulent near-wall region is known to be dominated by coherent structures. These near-wall coherent structures are observed to burst in a very intermittent fashion, exporting turbulent kinetic energy to the rest of the flow. In addition, they are closely related to invariant solutions known as exact coherent states (ECS), some of which display nonlinear critical layer dynamics (motions that are highly localized around the surface on which the streamwise velocity matches the wave speed of ECS). The present work aims to investigate temporal coherence in minimal channel flow relevant to turbulent bursting and critical layer dynamics and its connection to the instability of ECS. It is seen that the minimal channel turbulence displays frequencies very close to those displayed by an ECS family recently identified in the channel flow geometry. The frequencies of these ECS are determined by critical layer structures and thus might be described as "critical layer frequencies." While the bursting frequency is predominant near the wall, the ECS frequencies (critical layer frequencies) become predominant over the bursting frequency at larger distances from the wall, and increasingly so as Reynolds number increases. Turbulent bursts are classified into strong and relatively weak classes with respect to an intermittent approach to a lower branch ECS. This temporally intermittent approach is closely related to an intermittent low drag event, called hibernating turbulence, found in minimal and large domains. The relationship between the strong burst and the instability of the lower branch ECS is further discussed in state space. The state-space dynamics of strong bursts is very similar to that of the unstable manifolds of the lower branch ECS. In particular, strong bursting processes are always preceded by hibernation events. This precursor dynamics to strong turbulence may aid in development of more effective control schemes by a way of anticipating dynamics such as intermittent hibernating dynamics.

Equation of state and some structural and dynamical properties of the confined Lennard-Jones fluid into carbon nanotube: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Abbaspour, Mohsen; Akbarzadeh, Hamed; Salemi, Sirous; Abroodi, Mousarreza

2016-11-01

By considering the anisotropic pressure tensor, two separate equations of state (EoS) as functions of the density, temperature, and carbon nanotube (CNT) diameter have been proposed for the radial and axial directions for the confined Lennard-Jones (LJ) fluid into (11,11), (12,10), and (19,0) CNTs from 120 to 600 K using molecular dynamics (MD) simulations. We have also investigated the effects of the pore size, pore loading, chirality, and temperature on some of the structural and dynamical properties of the confined LJ fluid into (11,11), (12,10), (19,0), and (19,19) CNTs such as the radial density profile and self-diffusion coefficient. We have also determined the EoS for the confined LJ fluid into double and triple walled CNTs.

Hybrid state vector methods for structural dynamic and aeroelastic boundary value problems

NASA Technical Reports Server (NTRS)

Lehman, L. L.

1982-01-01

A computational technique is developed that is suitable for performing preliminary design aeroelastic and structural dynamic analyses of large aspect ratio lifting surfaces. The method proves to be quite general and can be adapted to solving various two point boundary value problems. The solution method, which is applicable to both fixed and rotating wing configurations, is based upon a formulation of the structural equilibrium equations in terms of a hybrid state vector containing generalized force and displacement variables. A mixed variational formulation is presented that conveniently yields a useful form for these state vector differential equations. Solutions to these equations are obtained by employing an integrating matrix method. The application of an integrating matrix provides a discretization of the differential equations that only requires solutions of standard linear matrix systems. It is demonstrated that matrix partitioning can be used to reduce the order of the required solutions. Results are presented for several example problems in structural dynamics and aeroelasticity to verify the technique and to demonstrate its use. These problems examine various types of loading and boundary conditions and include aeroelastic analyses of lifting surfaces constructed from anisotropic composite materials.

Competition between dynamic and structural disorder in a doped triangular antiferromagnet RbFe(MoO4)2

NASA Astrophysics Data System (ADS)

Smirnov, A. I.; Soldatov, T. A.; Petrenko, O. A.; Takata, A.; Kida, T.; Hagiwara, M.; Zhitomirsky, M. E.; Shapiro, A. Ya

2018-03-01

Magnetisation measurements and electron spin resonance (ESR) spectra of a doped quasi two dimensional (2D) antiferromagnet on a triangular lattice Rb1 ‑ x K x Fe(MoO4)2 reveal a crucial change of the ground state spin configuration and a disappearance of a characteristic 1/3-magnetisation plateau at x = 0.15. According to theory for triangular antiferromagnets with a weak random modulation of the exchange bonds, this is a result of the competition between the structural and dynamic disorders. The dynamic zero-point or thermal fluctuations are known to lift the degeneracy of the mean field ground state of a triangular antiferromagnet and cause the spin configuration to be the most collinear, while the static disorder provides another selection of the ground state, with the least collinear structure. Low-level doping (x ≤ 0.15) was found to decrease the Néel temperature and saturation field by only few percent, while the magnetisation plateau disappears completely and the spin configuration is drastically changed. ESR spectra confirm an impurity-induced change of the so-called Y-type structure to an inverted Y-structure for x = 0.15. For x = 0.075 the intermediate regime with the decrease of width and weakening of flattening of 1/3-plateau was found.

Quasibound states in a triple Gaussian potential

NASA Astrophysics Data System (ADS)

Reichl, L. E.; Porter, Max D.

2018-04-01

We derive the transmission probabilities and delay times, and identify quasibound state structures in an open quantum system consisting of three Gaussian potential energy peaks, a system whose classical scattering dynamics we show to be chaotic. Such open quantum systems can serve as models for nanoscale quantum devices and their wave dynamics are similar to electromagnetic wave dynamics in optical microcavities. We use a quantum web to determine energy regimes for which the system exhibits the quantum manifestations of chaos, and we show that the classical scattering dynamics contains a significant amount of chaos. We also derive an exact expression for the non-Hermitian Hamiltonian whose eigenvalues give quasibound state energies and lifetimes of the system.

Validating clustering of molecular dynamics simulations using polymer models.

PubMed

Phillips, Joshua L; Colvin, Michael E; Newsam, Shawn

2011-11-14

Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers.

Validating clustering of molecular dynamics simulations using polymer models

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers. PMID:22082218

Structured population dynamics: continuous size and discontinuous stage structures.

PubMed

Buffoni, Giuseppe; Pasquali, Sara

2007-04-01

A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

Stress-strain state of the structure in the service area of underground railway

NASA Astrophysics Data System (ADS)

Barabash, M.; Bashinsky, Y.; Korjakins, A.

2017-10-01

The paper focuses on numerical study how vibration due to underground trains influences the load-bearing building structures. Diagrams of vibration levels for monolithic floor slab depending on frequency are obtained. Levels of vibrations on floor slabs and columns are measured. The simulation of dynamic load from underground railway onto load-bearing building structures is presented as an example with account of load transmission through the soil. Recommendations for generation of design model in dynamic analysis of structure are provided.

On Cognition, Structured Sequence Processing, and Adaptive Dynamical Systems

NASA Astrophysics Data System (ADS)

Petersson, Karl Magnus

2008-11-01

Cognitive neuroscience approaches the brain as a cognitive system: a system that functionally is conceptualized in terms of information processing. We outline some aspects of this concept and consider a physical system to be an information processing device when a subclass of its physical states can be viewed as representational/cognitive and transitions between these can be conceptualized as a process operating on these states by implementing operations on the corresponding representational structures. We identify a generic and fundamental problem in cognition: sequentially organized structured processing. Structured sequence processing provides the brain, in an essential sense, with its processing logic. In an approach addressing this problem, we illustrate how to integrate levels of analysis within a framework of adaptive dynamical systems. We note that the dynamical system framework lends itself to a description of asynchronous event-driven devices, which is likely to be important in cognition because the brain appears to be an asynchronous processing system. We use the human language faculty and natural language processing as a concrete example through out.

Network structure of SiO2 and MgSiO3 in amorphous and liquid States

NASA Astrophysics Data System (ADS)

Lan, Mai Thi; Thuy Duong, Tran; Viet Huy, Nguyen; Van Hong, Nguyen

2017-03-01

Network structure of SiO2 and MgSiO3 at 300 K and 3200 K is investigated by molecular dynamics simulation and visualization of simulation data. Structural organization of SiO2 and MgSiO3 is clarified via analysis the short range order (SRO) and intermediate range order (IRO). Network topology is determined via analyzing the bond between structural units, the cluster of structural units as well as spatial distribution of structural units. The polyamorphism as well as structural and dynamic heterogeneities are also discussed in this work.

Crystal nucleation and metastable bcc phase in charged colloids: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Xinqiang; Sun, Zhiwei; Ouyang, Wenze; Xu, Shenghua

2018-05-01

The dynamic process of homogenous nucleation in charged colloids is investigated by brute-force molecular dynamics simulation. To check if the liquid-solid transition will pass through metastable bcc, simulations are performed at the state points that definitely lie in the phase region of thermodynamically stable fcc. The simulation results confirm that, in all of these cases, the preordered precursors, acting as the seeds of nucleation, always have predominant bcc symmetry consistent with Ostwald's step rule and the Alexander-McTague mechanism. However, the polymorph selection is not straightforward because the crystal structures formed are not often determined by the symmetry of intermediate precursors but have different characters under different state points. The region of the state point where bcc crystal structures of large enough size are formed during crystallization is narrow, which gives a reasonable explanation as to why the metastable bcc phase in charged colloidal suspensions is rarely detected in macroscopic experiments.

Revealing the fast atomic motion of network glasses.

PubMed

Ruta, B; Baldi, G; Chushkin, Y; Rufflé, B; Cristofolini, L; Fontana, A; Zanatta, M; Nazzani, F

2014-05-19

Still very little is known on the relaxation dynamics of glasses at the microscopic level due to the lack of experiments and theories. It is commonly believed that glasses are in a dynamical arrested state, with relaxation times too large to be observed on human time scales. Here we provide the experimental evidence that glasses display fast atomic rearrangements within a few minutes, even in the deep glassy state. Following the evolution of the structural relaxation in a sodium silicate glass, we find that this fast dynamics is accompanied by the absence of any detectable aging, suggesting a decoupling of the relaxation time and the viscosity in the glass. The relaxation time is strongly affected by the network structure with a marked increase at the mesoscopic scale associated with the ion-conducting pathways. Our results modify the conception of the glassy state and asks for a new microscopic theory.

Hierarchical folding free energy landscape of HP35 revealed by most probable path clustering.

PubMed

Jain, Abhinav; Stock, Gerhard

2014-07-17

Adopting extensive molecular dynamics simulations of villin headpiece protein (HP35) by Shaw and co-workers, a detailed theoretical analysis of the folding of HP35 is presented. The approach is based on the recently proposed most probable path algorithm which identifies the metastable states of the system, combined with dynamical coring of these states in order to obtain a consistent Markov state model. The method facilitates the construction of a dendrogram associated with the folding free-energy landscape of HP35, which reveals a hierarchical funnel structure and shows that the native state is rather a kinetic trap than a network hub. The energy landscape of HP35 consists of the entropic unfolded basin U, where the prestructuring of the protein takes place, the intermediate basin I, which is connected to U via the rate-limiting U → I transition state reflecting the formation of helix-1, and the native basin N, containing a state close to the NMR structure and a native-like state that exhibits enhanced fluctuations of helix-3. The model is in line with recent experimental observations that the intermediate and native states differ mostly in their dynamics (locked vs unlocked states). Employing dihedral angle principal component analysis, subdiffusive motion on a multidimensional free-energy surface is found.

Toward an atomistic description of the urea-denatured state of proteins.

PubMed

Candotti, Michela; Esteban-Martín, Santiago; Salvatella, Xavier; Orozco, Modesto

2013-04-09

We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea.

Toward an atomistic description of the urea-denatured state of proteins

PubMed Central

Candotti, Michela; Esteban-Martín, Santiago; Salvatella, Xavier; Orozco, Modesto

2013-01-01

We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea. PMID:23536295

The harmonic oscillator and nuclear physics

NASA Technical Reports Server (NTRS)

Rowe, D. J.

1993-01-01

The three-dimensional harmonic oscillator plays a central role in nuclear physics. It provides the underlying structure of the independent-particle shell model and gives rise to the dynamical group structures on which models of nuclear collective motion are based. It is shown that the three-dimensional harmonic oscillator features a rich variety of coherent states, including vibrations of the monopole, dipole, and quadrupole types, and rotations of the rigid flow, vortex flow, and irrotational flow types. Nuclear collective states exhibit all of these flows. It is also shown that the coherent state representations, which have their origins in applications to the dynamical groups of the simple harmonic oscillator, can be extended to vector coherent state representations with a much wider range of applicability. As a result, coherent state theory and vector coherent state theory become powerful tools in the application of algebraic methods in physics.

Anti-Stokes resonant x-ray Raman scattering for atom specific and excited state selective dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunnus, Kristjan; Josefsson, Ida; Rajkovic, Ivan

Here, ultrafast electronic and structural dynamics of matter govern rate and selectivity of chemical reactions, as well as phase transitions and efficient switching in functional materials. Since x-rays determine electronic and structural properties with elemental, chemical, orbital and magnetic selectivity, short pulse x-ray sources have become central enablers of ultrafast science. Despite of these strengths, ultrafast x-rays have been poor at picking up excited state moieties from the unexcited ones. With time-resolved anti-Stokes resonant x-ray Raman scattering (AS-RXRS) performed at the LCLS, and ab initio theory we establish background free excited state selectivity in addition to the elemental, chemical, orbitalmore » and magnetic selectivity of x-rays. This unparalleled selectivity extracts low concentration excited state species along the pathway of photo induced ligand exchange of Fe(CO)5 in ethanol. Conceptually a full theoretical treatment of all accessible insights to excited state dynamics with AS-RXRS with transform-limited x-ray pulses is given—which will be covered experimentally by upcoming transform-limited x-ray sources.« less

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy

NASA Astrophysics Data System (ADS)

Weichman, Marissa L.; Devine, Jessalyn A.; Babin, Mark C.; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M.

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH3OH → HF + CH3O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH3OHF- anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy.

PubMed

Weichman, Marissa L; DeVine, Jessalyn A; Babin, Mark C; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH 3 OH → HF + CH 3 O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH 3 OHF - anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Anti-Stokes resonant x-ray Raman scattering for atom specific and excited state selective dynamics

DOE PAGES

Kunnus, Kristjan; Josefsson, Ida; Rajkovic, Ivan; ...

2016-10-07

Here, ultrafast electronic and structural dynamics of matter govern rate and selectivity of chemical reactions, as well as phase transitions and efficient switching in functional materials. Since x-rays determine electronic and structural properties with elemental, chemical, orbital and magnetic selectivity, short pulse x-ray sources have become central enablers of ultrafast science. Despite of these strengths, ultrafast x-rays have been poor at picking up excited state moieties from the unexcited ones. With time-resolved anti-Stokes resonant x-ray Raman scattering (AS-RXRS) performed at the LCLS, and ab initio theory we establish background free excited state selectivity in addition to the elemental, chemical, orbitalmore » and magnetic selectivity of x-rays. This unparalleled selectivity extracts low concentration excited state species along the pathway of photo induced ligand exchange of Fe(CO)5 in ethanol. Conceptually a full theoretical treatment of all accessible insights to excited state dynamics with AS-RXRS with transform-limited x-ray pulses is given—which will be covered experimentally by upcoming transform-limited x-ray sources.« less

Protonation States in molecular dynamics simulations of peptide folding and binding.

PubMed

Ben-Shimon, Avraham; Shalev, Deborah E; Niv, Masha Y

2013-01-01

Peptides are important signaling modules, acting both as individual hormones and as parts of larger molecules, mediating their protein-protein interactions. Many peptidic and peptidomimetic drugs have reached the marketplace and opportunities for peptide-based drug discovery are on the rise. pH-dependent behavior of peptides is well documented in the context of misfolding diseases and peptide translocation. Changes in the protonation states of peptide residues often have a crucial effect on a peptide's structure, dynamics and function, which may be exploited for biotechnological applications. The current review surveys the increasing levels of sophistication in the treatment of protonation states in computational studies involving peptides. Specifically we describe I) the common practice of assigning a single protonation state and using it throughout the dynamic simulation, II) approaches that consider multiple protonation states and compare computed observables to experimental ones, III) constant pH molecular dynamics methods that couple changes in protonation states with conformational dynamics "on the fly". Applications of conformational dynamics treatment of peptides in the context of binding, folding and interactions with the membrane are presented, illustrating the growing body of work in this field and highlighting the importance of careful handling of protonation states of peptidic residues.

Chemical structure and dynamics: Annual report 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colson, S.D.; McDowell, R.S.

1997-03-01

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can bemore » brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.« less

Structure and dynamics of AMPA receptor GluA2 in resting, pre-open and desensitized states

PubMed Central

Dürr, Katharina L.; Chen, Lei; Stein, Richard A.; De Zorzi, Rita; MihaelaFolea, I.; Walz, Thomas; Mchaourab, Hassane S.; Gouaux, Eric

2014-01-01

Summary Ionotropic glutamate receptors (iGluRs) mediate the majority of fast excitatory signaling in the nervous system. Despite the profound importance of iGluRs in the nervous system, little is known about the structures and dynamics of intact receptors in distinct functional states. Here we elucidate the structures of the intact GluA2 AMPA receptor in an apo resting/closed state, in an activated/pre-open state bound with the partial agonists and a positive allosteric modulator and in a desensitized/closed state in complex with FW alone. To probe the conformational properties of these states, we carried out double electron-electron resonance experiments on cysteine mutants and cryo-electron microscopy studies. We show how agonist binding modulates the conformation of the ligand binding domain 'layer' of the intact receptors and how, upon desensitization, the receptor undergoes large conformational rearrangements of amino-terminal and ligand-binding domains. We define mechanistic principles by which to understand antagonism, activation and desensitization in AMPA iGluRs. PMID:25109876

Effects of state recovery on creep buckling under variable loading

NASA Technical Reports Server (NTRS)

Robinson, D. N.; Arnold, S. M.

1986-01-01

Structural alloys embody internal mechanisms that allow recovery of state with varying stress and elevated temperature, i.e., they can return to a softer state following periods of hardening. Such material behavior is known to strongly influence structural response under some important thermomechanical loadings, for example, that involving thermal ratchetting. The influence of dynamic and thermal recovery on the creep buckling of a column under variable loading is investigated. The column is taken as the idealized (Shanley) sandwich column. The constitutive model, unlike the commonly employed Norton creep model, incorporates a representation of both dynamic and thermal (state) recovery. The material parameters of the constitutive model are chosen to characterize Narloy Z, a representative copper alloy used in thrust nozzle liners of reusable rocket engines. Variable loading histories include rapid cyclic unloading/reloading sequences and intermittent reductions of load for extended periods of time; these are superimposed on a constant load. The calculated results show that state recovery significantly affects creep buckling under variable loading. Structural alloys embody internal mechanisms that allow recovery of state with varying stress and time.

Thermostabilization of the β1-adrenergic receptor correlates with increased entropy of the inactive state.

PubMed

Niesen, Michiel J M; Bhattacharya, Supriyo; Grisshammer, Reinhard; Tate, Christopher G; Vaidehi, Nagarajan

2013-06-20

The dynamic nature of GPCRs is a major hurdle in their purification and crystallization. Thermostabilization can facilitate GPCR structure determination, as has been shown by the structure of the thermostabilized β1-adrenergic receptor (β1AR) mutant, m23-β1AR, which has been thermostabilized in the inactive state. However, it is unclear from the structure how the six thermostabilizing mutations in m23-β1AR affect receptor dynamics. We have used molecular dynamics simulations in explicit solvent to compare the conformational ensembles for both wild type β1AR (wt-β1AR) and m23-β1AR. Thermostabilization results in an increase in the number of accessible microscopic conformational states within the inactive state ensemble, effectively increasing the side chain entropy of the inactive state at room temperature, while suppressing large-scale main chain conformational changes that lead to activation. We identified several diverse mechanisms of thermostabilization upon mutation. These include decrease of long-range correlated movement between residues in the G-protein coupling site to the extracellular region (Y227A(5.58), F338M(7.48)), formation of new hydrogen bonds (R68S), and reduction of local stress (Y227(5.58), F327(7.37), and F338(7.48)). This study provides insights into microscopic mechanisms underlying thermostability that leads to an understanding of the effect of these mutations on the structure of the receptor.

Imaging the equilibrium state and magnetization dynamics of partially built hard disk write heads

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valkass, R. A. J., E-mail: rajv202@ex.ac.uk; Yu, W.; Shelford, L. R.

Four different designs of partially built hard disk write heads with a yoke comprising four repeats of NiFe (1 nm)/CoFe (50 nm) were studied by both x-ray photoemission electron microscopy (XPEEM) and time-resolved scanning Kerr microscopy (TRSKM). These techniques were used to investigate the static equilibrium domain configuration and the magnetodynamic response across the entire structure, respectively. Simulations and previous TRSKM studies have made proposals for the equilibrium domain configuration of similar structures, but no direct observation of the equilibrium state of the writers has yet been made. In this study, static XPEEM images of the equilibrium state of writer structures weremore » acquired using x-ray magnetic circular dichroism as the contrast mechanism. These images suggest that the crystalline anisotropy dominates the equilibrium state domain configuration, but competition with shape anisotropy ultimately determines the stability of the equilibrium state. Dynamic TRSKM images were acquired from nominally identical devices. These images suggest that a longer confluence region may hinder flux conduction from the yoke into the pole tip: the shorter confluence region exhibits clear flux beaming along the symmetry axis, whereas the longer confluence region causes flux to conduct along one edge of the writer. The observed variations in dynamic response agree well with the differences in the equilibrium magnetization configuration visible in the XPEEM images, confirming that minor variations in the geometric design of the writer structure can have significant effects on the process of flux beaming.« less

Dynamical differences of hemoglobin and the ionotropic glutamate receptor in different states revealed by a new dynamics alignment method.

PubMed

Tobi, Dror

2017-08-01

A new algorithm for comparison of protein dynamics is presented. Compared protein structures are superposed and their modes of motions are calculated using the anisotropic network model. The obtained modes are aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. Dynamical comparison of hemoglobin in the T and R2 states reveals that the dynamics of the allosteric effector 2,3-bisphosphoglycerate binding site is different in the two states. These differences can contribute to the selectivity of the effector to the T state. Similar comparison of the ionotropic glutamate receptor in the kainate+(R,R)-2b and ZK bound states reveals that the kainate+(R,R)-2b bound states slow modes describe upward motions of ligand binding domain and the transmembrane domain regions. Such motions may lead to the opening of the receptor. The upper lobes of the LBDs of the ZK bound state have a smaller interface with the amino terminal domains above them and have a better ability to move together. The present study exemplifies the use of dynamics comparison as a tool to study protein function. Proteins 2017; 85:1507-1517. © 2014 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Ecosystem Restoration: Fact or Fancy?

Treesearch

John A. Stanturf; Callie J. Schweitzer; Stephen H. Schoenholtz; James P. Barnett; Charles K. McMahon; Donald J. Tomszak

1998-01-01

Ecological restoration is generally accepted as the reestablishment of natural ecological processes that produce certain dynamic ecosystem properties of structure, function, and processes. But restore to what? The most frequently used conceptual model for the restoration process is the shift of conditions from some current (degraded) dynamic state to some past dynamic...

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

PubMed

Sarti, Edoardo; Gladich, Ivan; Zamuner, Stefano; Correia, Bruno E; Laio, Alessandro

2016-09-01

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312-1320. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Macroscopic description of complex adaptive networks coevolving with dynamic node states

NASA Astrophysics Data System (ADS)

Wiedermann, Marc; Donges, Jonathan F.; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.

Macroscopic description of complex adaptive networks coevolving with dynamic node states.

PubMed

Wiedermann, Marc; Donges, Jonathan F; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.

One size does not fit all: Adapting mark-recapture and occupancy models for state uncertainty

USGS Publications Warehouse

Kendall, W.L.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

2009-01-01

Multistate capture?recapture models continue to be employed with greater frequency to test hypotheses about metapopulation dynamics and life history, and more recently disease dynamics. In recent years efforts have begun to adjust these models for cases where there is uncertainty about an animal?s state upon capture. These efforts can be categorized into models that permit misclassification between two states to occur in either direction or one direction, where state is certain for a subset of individuals or is always uncertain, and where estimation is based on one sampling occasion per period of interest or multiple sampling occasions per period. State uncertainty also arises in modeling patch occupancy dynamics. I consider several case studies involving bird and marine mammal studies that illustrate how misclassified states can arise, and outline model structures for properly utilizing the data that are produced. In each case misclassification occurs in only one direction (thus there is a subset of individuals or patches where state is known with certainty), and there are multiple sampling occasions per period of interest. For the cases involving capture?recapture data I allude to a general model structure that could include each example as a special case. However, this collection of cases also illustrates how difficult it is to develop a model structure that can be directly useful for answering every ecological question of interest and account for every type of data from the field.

Conformational dynamics of a protein in the folded and the unfolded state

NASA Astrophysics Data System (ADS)

Fitter, Jörg

2003-08-01

In a quasielastic neutron scattering experiment, the picosecond dynamics of α-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D 2O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 Å; unfolded state, 1.8 Å). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

Membrane solid-state NMR in Canada: A historical perspective.

PubMed

Auger, Michèle

2017-11-01

This manuscript presents an overview of more than 40years of membrane solid-state nuclear magnetic resonance (NMR) research in Canada. This technique is a method of choice for the study of the structure and dynamics of lipid bilayers; bilayer interactions with a variety of molecules such as membrane peptides, membrane proteins and drugs; and to investigate membrane peptide and protein structure, dynamics, and topology. Canada has a long tradition in this field of research, starting with pioneering work on natural and model membranes in the 1970s in a context of emergence of biophysics in the country. The 1980s and 1990s saw an emphasis on studying lipid structures and dynamics, and peptide-lipid and protein-lipid interactions. The study of bicelles began in the 1990s, and in the 2000s there was a rise in the study of membrane protein structures. Novel perspectives include using dynamic nuclear polarization (DNP) for membrane studies and using NMR in live cells. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Topological solitons in helical strings

NASA Astrophysics Data System (ADS)

Nisoli, Cristiano; Balatsky, Alexander V.

2015-06-01

The low-energy physics of (quasi)degenerate one-dimensional systems is typically understood as the particle-like dynamics of kinks between stable, ordered structures. Such dynamics, we show, becomes highly nontrivial when the ground states are topologically constrained: a dynamics of the domains rather than on the domains which the kinks separate. Motivated by recently reported observations of charged polymers physio-adsorbed on nanotubes, we study kinks between helical structures of a string wrapping around a cylinder. While their motion cannot be disentangled from domain dynamics, and energy and momentum is not concentrated in the solitons, the dynamics of the domains can be folded back into a particle-like description of the local excitations.

General properties of quantum optical systems in a strong field limit

NASA Technical Reports Server (NTRS)

Chumakov, S. M.; Klimov, Andrei B.

1994-01-01

We investigate the dynamics of an arbitrary atomic system (n-level atoms or many n-level atoms) interacting with a resonant quantized mode of an em field. If the initial field state is a coherent state with a large photon number then the system dynamics possesses some general features, independently of the particular structure of the atomic system. Namely, trapping states, factorization of the wave function, collapses and revivals of the atomic energy oscillations are discussed.

Ultrafast internal conversion dynamics of highly excited pyrrole studied with VUV/UV pump probe spectroscopy.

PubMed

Horton, Spencer L; Liu, Yusong; Chakraborty, Pratip; Matsika, Spiridoula; Weinacht, Thomas

2017-02-14

We study the relaxation dynamics of pyrrole after excitation with an 8 eV pump pulse to a state just 0.2 eV below the ionization potential using vacuum ultraviolet/ultraviolet pump probe spectroscopy. Our measurements in conjunction with electronic structure calculations indicate that pyrrole undergoes rapid internal conversion to the ground state in less than 300 fs. We find that internal conversion to the ground state dominates over dissociation.

Projections of limiting states for load-bearing structures of reflectors made of polymer composites

NASA Astrophysics Data System (ADS)

Doronin, S. V.

2017-12-01

This paper deals with limiting states typical for reflector antennas for terrestrial satellite communication systems. Reflectors made of polymer composites are studied. These limiting states are projected by results of the numerical analysis of the stress and strain states. The analysis is executed for reflectors under conditions of static and dynamic loading. It takes into account both overshoot of the state variables of allowed level and the processes of long-term structural material degradation.

New insights into photodissociation dynamics of cyclobutanone from the AIMS dynamic simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Lihong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn

2016-04-14

In this work, the combined electronic structure calculations and non-adiabatic dynamics simulations were performed for understanding mechanistic photodissociation of cyclobutanone at ∼248 nm. Besides the stationary and intersection structures reported before, two new conical intersections between the ground (S{sub 0}) and the first excited singlet (S{sub 1}) states were determined in the present study, which were confirmed to be the new S{sub 1} → S{sub 0} funnels by the ab initio multiple spawning dynamic simulation, giving rise to products in the S{sub 0} state selectively. The time evolution of the S{sub 1} electronic population was fitted with the pure exponentialmore » formulae, from which the S{sub 1} lifetime was estimated to be 484.0 fs. The time constant for the S{sub 1} α-cleavage is calculated to be 176.6 fs, which is based on the present dynamics simulation. As a result of the ultrafast S{sub 1} processes, the statistical distribution of the excess energies is prevented in the S{sub 1} state. The S{sub 1} dynamic effect (the nonergodic behavior) was predicted to be an important factor that is responsible for the wavelength dependence of the branching ratio of photodissociation products, which will be discussed in detail.« less

A Time Integration Algorithm Based on the State Transition Matrix for Structures with Time Varying and Nonlinear Properties

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2003-01-01

A variable order method of integrating the structural dynamics equations that is based on the state transition matrix has been developed. The method has been evaluated for linear time variant and nonlinear systems of equations. When the time variation of the system can be modeled exactly by a polynomial it produces nearly exact solutions for a wide range of time step sizes. Solutions of a model nonlinear dynamic response exhibiting chaotic behavior have been computed. Accuracy of the method has been demonstrated by comparison with solutions obtained by established methods.

Lactose binding to galectin-1 modulates structural dynamics, increases conformational entropy, and occurs with apparent negative cooperativity.

PubMed

Nesmelova, Irina V; Ermakova, Elena; Daragan, Vladimir A; Pang, Mabel; Menéndez, Margarita; Lagartera, Laura; Solís, Dolores; Baum, Linda G; Mayo, Kevin H

2010-04-16

Galectins are a family of lectins with a conserved carbohydrate recognition domain that interacts with beta-galactosides. By binding cell surface glycoconjugates, galectin-1 (gal-1) is involved in cell adhesion and migration processes and is an important regulator of tumor angiogenesis. Here, we used heteronuclear NMR spectroscopy and molecular modeling to investigate lactose binding to gal-1 and to derive solution NMR structures of gal-1 in the lactose-bound and unbound states. Structure analysis shows that the beta-strands and loops around the lactose binding site, which are more open and dynamic in the unbound state, fold in around the bound lactose molecule, dampening internal motions at that site and increasing motions elsewhere throughout the protein to contribute entropically to the binding free energy. CD data support the view of an overall more open structure in the lactose-bound state. Analysis of heteronuclear single quantum coherence titration binding data indicates that lactose binds the two carbohydrate recognition domains of the gal-1 dimer with negative cooperativity, in that the first lactose molecule binds more strongly (K(1)=21+/-6 x 10(3) M(-1)) than the second (K(2)=4+/-2 x 10(3) M(-1)). Isothermal calorimetry data fit using a sequential binding model present a similar picture, yielding K(1)=20+/-10 x 10(3) M(-1) and K(2)=1.67+/-0.07 x 10(3) M(-1). Molecular dynamics simulations provide insight into structural dynamics of the half-loaded lactose state and, together with NMR data, suggest that lactose binding at one site transmits a signal through the beta-sandwich and loops to the second binding site. Overall, our results provide new insight into gal-1 structure-function relationships and to protein-carbohydrate interactions in general. Copyright (c) 2010. Published by Elsevier Ltd.

A juvenile-adult population model: climate change, cannibalism, reproductive synchrony, and strong Allee effects.

PubMed

Veprauskas, Amy; Cushing, J M

2017-03-01

We study a discrete time, structured population dynamic model that is motivated by recent field observations concerning certain life history strategies of colonial-nesting gulls, specifically the glaucous-winged gull (Larus glaucescens). The model focuses on mechanisms hypothesized to play key roles in a population's response to degraded environment resources, namely, increased cannibalism and adjustments in reproductive timing. We explore the dynamic consequences of these mechanics using a juvenile-adult structure model. Mathematically, the model is unusual in that it involves a high co-dimension bifurcation at [Formula: see text] which, in turn, leads to a dynamic dichotomy between equilibrium states and synchronized oscillatory states. We give diagnostic criteria that determine which dynamic is stable. We also explore strong Allee effects caused by positive feedback mechanisms in the model and the possible consequence that a cannibalistic population can survive when a non-cannibalistic population cannot.

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

The role of protein dynamics in the evolution of new enzyme function.

PubMed

Campbell, Eleanor; Kaltenbach, Miriam; Correy, Galen J; Carr, Paul D; Porebski, Benjamin T; Livingstone, Emma K; Afriat-Jurnou, Livnat; Buckle, Ashley M; Weik, Martin; Hollfelder, Florian; Tokuriki, Nobuhiko; Jackson, Colin J

2016-11-01

Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.

Cognitive Flexibility through Metastable Neural Dynamics Is Disrupted by Damage to the Structural Connectome.

PubMed

Hellyer, Peter J; Scott, Gregory; Shanahan, Murray; Sharp, David J; Leech, Robert

2015-06-17

Current theory proposes that healthy neural dynamics operate in a metastable regime, where brain regions interact to simultaneously maximize integration and segregation. Metastability may confer important behavioral properties, such as cognitive flexibility. It is increasingly recognized that neural dynamics are constrained by the underlying structural connections between brain regions. An important challenge is, therefore, to relate structural connectivity, neural dynamics, and behavior. Traumatic brain injury (TBI) is a pre-eminent structural disconnection disorder whereby traumatic axonal injury damages large-scale connectivity, producing characteristic cognitive impairments, including slowed information processing speed and reduced cognitive flexibility, that may be a result of disrupted metastable dynamics. Therefore, TBI provides an experimental and theoretical model to examine how metastable dynamics relate to structural connectivity and cognition. Here, we use complementary empirical and computational approaches to investigate how metastability arises from the healthy structural connectome and relates to cognitive performance. We found reduced metastability in large-scale neural dynamics after TBI, measured with resting-state functional MRI. This reduction in metastability was associated with damage to the connectome, measured using diffusion MRI. Furthermore, decreased metastability was associated with reduced cognitive flexibility and information processing. A computational model, defined by empirically derived connectivity data, demonstrates how behaviorally relevant changes in neural dynamics result from structural disconnection. Our findings suggest how metastable dynamics are important for normal brain function and contingent on the structure of the human connectome. Copyright © 2015 the authors 0270-6474/15/359050-14$15.00/0.

The Role of Linkers in the Excited-State Dynamic Planarization Processes of Macrocyclic Oligothiophene 12-Mers.

PubMed

Kim, Woojae; Sung, Jooyoung; Park, Kyu Hyung; Shimizu, Hideyuki; Imamura, Mika; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho

2015-11-05

Linkers adjoining chromophores play an important role in modulating the structure of conjugated systems, which is bound up with their photophysical properties. However, to date, the focus of works dealing with linker effects was limited only to linear π-conjugated materials, and there have been no detailed studies on cyclic counterparts. Herein we report the linker effects on the dynamic planarization processes of π-conjugated macrocyclic oligothiophene 12-mers, where the different ratio between ethynylene and vinylene linkers was chosen to control the backbone rigidity. By analyzing transient fluorescence spectra, we demonstrate that the connecting linkers play a crucial role in the excited-state dynamics of cyclic conjugated systems. Faster dynamic planarization, longer exciton delocalization length, and higher degree of planarity were observed in vinylene inserted cyclic oligothiophenes. Molecular dynamics simulations and density functional theory calculations also stress the importance of the role of linkers in modulating the structure of cyclic oligothiophenes.

Ultrafast X-Ray Spectroscopy of Conical Intersections

NASA Astrophysics Data System (ADS)

Neville, Simon P.; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

2018-06-01

Ongoing developments in ultrafast x-ray sources offer powerful new means of probing the complex nonadiabatically coupled structural and electronic dynamics of photoexcited molecules. These non-Born-Oppenheimer effects are governed by general electronic degeneracies termed conical intersections, which play a key role, analogous to that of a transition state, in the electronic-nuclear dynamics of excited molecules. Using high-level ab initio quantum dynamics simulations, we studied time-resolved x-ray absorption (TRXAS) and photoelectron spectroscopy (TRXPS) of the prototypical unsaturated organic chromophore, ethylene, following excitation to its S2(π π*) state. The TRXAS, in particular, is highly sensitive to all aspects of the ensuing dynamics. These x-ray spectroscopies provide a clear signature of the wave packet dynamics near conical intersections, related to charge localization effects driven by the nuclear dynamics. Given the ubiquity of charge localization in excited state dynamics, we believe that ultrafast x-ray spectroscopies offer a unique and powerful route to the direct observation of dynamics around conical intersections.

First-Principles Study of the Structural, Optical, Dynamical and Thermodynamic Properties of BaZnO2 Under Pressure

NASA Astrophysics Data System (ADS)

Wang, Yi-Xian; Hu, Cui-E.; Chen, Yang-Mei; Cheng, Yan; Ji, Guang-Fu

2016-11-01

The structural, optical, dynamical, and thermodynamic properties of BaZnO2 under pressure are studied based on the density functional theory. The calculated structural parameters are consistent with the available experimental data. In the ground state, the electronic band structure and density of states indicate that BaZnO2 is an insulator with a direct gap of 2.2 eV. The Mulliken charges are also analyzed to characterize the bonding property. After the structural relaxation, the optical properties are studied. It is found that the dielectric function of E Vert x and EVert y are isotropic, whereas the EVert x and EVert z are anisotropic. The effect of pressure on the energy-loss function in the ultraviolet region becomes more obvious as the pressure increases. Furthermore, the dynamical properties under different pressures are investigated using the finite displacement method. We find that the P3121 phase of BaZnO2 is dynamically stable under the pressure ranging from 0 GPa to 30 GPa. The phonon dispersion curves, phonon density of states, vibrational modes and atoms that contribute to these vibrations at {{\\varvec{Γ }}} point under different pressures are also reported in this work. Finally, by employing the quasi-harmonic approximation, the thermodynamic properties such as the temperature dependence of the thermal expansion coefficient, specific heat, entropy and Gibbs free energy under different pressures are investigated. It is found that the influences of the temperature on the heat capacity are much more significant than that of the pressure on it.

Global Dynamics of Proteins: Bridging Between Structure and Function

PubMed Central

Bahar, Ivet; Lezon, Timothy R.; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold. PMID:20192781

Global dynamics of proteins: bridging between structure and function.

PubMed

Bahar, Ivet; Lezon, Timothy R; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.

Coevolution of dynamical states and interactions in dynamic networks

NASA Astrophysics Data System (ADS)

Zimmermann, Martín G.; Eguíluz, Víctor M.; San Miguel, Maxi

2004-06-01

We explore the coupled dynamics of the internal states of a set of interacting elements and the network of interactions among them. Interactions are modeled by a spatial game and the network of interaction links evolves adapting to the outcome of the game. As an example, we consider a model of cooperation in which the adaptation is shown to facilitate the formation of a hierarchical interaction network that sustains a highly cooperative stationary state. The resulting network has the characteristics of a small world network when a mechanism of local neighbor selection is introduced in the adaptive network dynamics. The highly connected nodes in the hierarchical structure of the network play a leading role in the stability of the network. Perturbations acting on the state of these special nodes trigger global avalanches leading to complete network reorganization.

Transferring the entatic-state principle to copper photochemistry

NASA Astrophysics Data System (ADS)

Dicke, B.; Hoffmann, A.; Stanek, J.; Rampp, M. S.; Grimm-Lebsanft, B.; Biebl, F.; Rukser, D.; Maerz, B.; Göries, D.; Naumova, M.; Biednov, M.; Neuber, G.; Wetzel, A.; Hofmann, S. M.; Roedig, P.; Meents, A.; Bielecki, J.; Andreasson, J.; Beyerlein, K. R.; Chapman, H. N.; Bressler, C.; Zinth, W.; Rübhausen, M.; Herres-Pawlis, S.

2018-03-01

The entatic state denotes a distorted coordination geometry of a complex from its typical arrangement that generates an improvement to its function. The entatic-state principle has been observed to apply to copper electron-transfer proteins and it results in a lowering of the reorganization energy of the electron-transfer process. It is thus crucial for a multitude of biochemical processes, but its importance to photoactive complexes is unexplored. Here we study a copper complex—with a specifically designed constraining ligand geometry—that exhibits metal-to-ligand charge-transfer state lifetimes that are very short. The guanidine-quinoline ligand used here acts on the bis(chelated) copper(I) centre, allowing only small structural changes after photoexcitation that result in very fast structural dynamics. The data were collected using a multimethod approach that featured time-resolved ultraviolet-visible, infrared and X-ray absorption and optical emission spectroscopy. Through supporting density functional calculations, we deliver a detailed picture of the structural dynamics in the picosecond-to-nanosecond time range.

Conformational Dynamics of Insulin

PubMed Central

Hua, Qing-Xin; Jia, Wenhua; Weiss, Michael A.

2011-01-01

We have exploited a prandial insulin analog to elucidate the underlying structure and dynamics of insulin as a monomer in solution. A model was provided by insulin lispro (the active component of Humalog®; Eli Lilly and Co.). Whereas NMR-based modeling recapitulated structural relationships of insulin crystals (T-state protomers), dynamic anomalies were revealed by amide-proton exchange kinetics in D2O. Surprisingly, the majority of hydrogen bonds observed in crystal structures are only transiently maintained in solution, including key T-state-specific inter-chain contacts. Long-lived hydrogen bonds (as defined by global exchange kinetics) exist only at a subset of four α-helical sites (two per chain) flanking an internal disulfide bridge (cystine A20–B19); these sites map within the proposed folding nucleus of proinsulin. The anomalous flexibility of insulin otherwise spans its active surface and may facilitate receptor binding. Because conformational fluctuations promote the degradation of pharmaceutical formulations, we envisage that “dynamic re-engineering” of insulin may enable design of ultra-stable formulations for humanitarian use in the developing world. PMID:22649374

Ab initio study of the structure and dynamics of bulk liquid Fe

NASA Astrophysics Data System (ADS)

Marqués, M.; González, L. E.; González, D. J.

2015-10-01

Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

NASA Astrophysics Data System (ADS)

Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

2017-10-01

Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

Using resonant x-ray scattering to determine how structure controls the charge generation process in PCPDTBT:PC70BM solar cells

NASA Astrophysics Data System (ADS)

Pope, Michael; Waldrip, Matthew; Ferron, Thomas; Collins, Brian

Increased solar power conversion efficiencies to 12% in bulk heterojunction organic photovoltaics (OPVs) continue to brighten their prospects as an economically viable source of solar energy. It is known that OPV performance can be enhanced through processing additives that change the nanostructure. We track these critical structure-property relationships in the OPV system PCPDTBT:PC70BM while varying the amount of DIO additive. Resonant Soft X-ray Scattering reveals domain purity, domain size, and molecular orientation to highlight the system's complex dependence on DIO concentration. We will show the effect the resulting structure has on charge generation and recombination via in-situ transient and steady state optoelectronic measurements. By measuring structure, excited state dynamics and device performance all on the same sample enables direct relationships to be measured. We show that the appropriate balance of crystallinity, domain size and domain purity are important for optimized excited state dynamics and device performance.

Dynamics of one-state downhill protein folding.

PubMed

Li, Peng; Oliva, Fabiana Y; Naganathan, Athi N; Muñoz, Victor

2009-01-06

The small helical protein BBL has been shown to fold and unfold in the absence of a free energy barrier according to a battery of quantitative criteria in equilibrium experiments, including probe-dependent equilibrium unfolding, complex coupling between denaturing agents, characteristic DSC thermogram, gradual melting of secondary structure, and heterogeneous atom-by-atom unfolding behaviors spanning the entire unfolding process. Here, we present the results of nanosecond T-jump experiments probing backbone structure by IR and end-to-end distance by FRET. The folding dynamics observed with these two probes are both exponential with common relaxation times but have large differences in amplitude following their probe-dependent equilibrium unfolding. The quantitative analysis of amplitude and relaxation time data for both probes shows that BBL folding dynamics are fully consistent with the one-state folding scenario and incompatible with alternative models involving one or several barrier crossing events. At 333 K, the relaxation time for BBL is 1.3 micros, in agreement with previous folding speed limit estimates. However, late folding events at room temperature are an order of magnitude slower (20 micros), indicating a relatively rough underlying energy landscape. Our results in BBL expose the dynamic features of one-state folding and chart the intrinsic time-scales for conformational motions along the folding process. Interestingly, the simple self-averaging folding dynamics of BBL are the exact dynamic properties required in molecular rheostats, thus supporting a biological role for one-state folding.

Computing the structural influence matrix for biological systems.

PubMed

Giordano, Giulia; Cuba Samaniego, Christian; Franco, Elisa; Blanchini, Franco

2016-06-01

We consider the problem of identifying structural influences of external inputs on steady-state outputs in a biological network model. We speak of a structural influence if, upon a perturbation due to a constant input, the ensuing variation of the steady-state output value has the same sign as the input (positive influence), the opposite sign (negative influence), or is zero (perfect adaptation), for any feasible choice of the model parameters. All these signs and zeros can constitute a structural influence matrix, whose (i, j) entry indicates the sign of steady-state influence of the jth system variable on the ith variable (the output caused by an external persistent input applied to the jth variable). Each entry is structurally determinate if the sign does not depend on the choice of the parameters, but is indeterminate otherwise. In principle, determining the influence matrix requires exhaustive testing of the system steady-state behaviour in the widest range of parameter values. Here we show that, in a broad class of biological networks, the influence matrix can be evaluated with an algorithm that tests the system steady-state behaviour only at a finite number of points. This algorithm also allows us to assess the structural effect of any perturbation, such as variations of relevant parameters. Our method is applied to nontrivial models of biochemical reaction networks and population dynamics drawn from the literature, providing a parameter-free insight into the system dynamics.

A Quantitative Method for the Analysis of Nomothetic Relationships between Idiographic Structures: Dynamic Patterns Create Attractor States for Sustained Posttreatment Change

ERIC Educational Resources Information Center

Fisher, Aaron J.; Newman, Michelle G.; Molenaar, Peter C. M.

2011-01-01

Objective: The present article aimed to demonstrate that the establishment of dynamic patterns during the course of psychotherapy can create attractor states for continued adaptive change following the conclusion of treatment. Method: This study is a secondary analysis of T. D. Borkovec and E. Costello (1993). Of the 55 participants in the…

Dynamic functional-structural coupling within acute functional state change phases: Evidence from a depression recognition study.

PubMed

Bi, Kun; Hua, Lingling; Wei, Maobin; Qin, Jiaolong; Lu, Qing; Yao, Zhijian

2016-02-01

Dynamic functional-structural connectivity (FC-SC) coupling might reflect the flexibility by which SC relates to functional connectivity (FC). However, during the dynamic acute state change phases of FC, the relationship between FC and SC may be distinctive and embody the abnormality inherent in depression. This study investigated the depression-related inter-network FC-SC coupling within particular dynamic acute state change phases of FC. Magnetoencephalography (MEG) and diffusion tensor imaging (DTI) data were collected from 26 depressive patients (13 women) and 26 age-matched controls (13 women). We constructed functional brain networks based on MEG data and structural networks from DTI data. The dynamic connectivity regression algorithm was used to identify the state change points of a time series of inter-network FC. The time period of FC that contained change points were partitioned into types of dynamic phases (acute rising phase, acute falling phase,acute rising and falling phase and abrupt FC variation phase) to explore the inter-network FC-SC coupling. The selected FC-SC couplings were then fed into the support vector machine (SVM) for depression recognition. The best discrimination accuracy was 82.7% (P=0.0069) with FC-SC couplings, particularly in the acute rising phase of FC. Within the FC phases of interest, the significant discriminative network pair was related to the salience network vs ventral attention network (SN-VAN) (P=0.0126) during the early rising phase (70-170ms). This study suffers from a small sample size, and the individual acute length of the state change phases was not considered. The increased values of significant discriminative vectors of FC-SC coupling in depression suggested that the capacity to process negative emotion might be more directly related to the SC abnormally and be indicative of more stringent and less dynamic brain function in SN-VAN, especially in the acute rising phase of FC. We demonstrated that depressive brain dysfunctions could be better characterized by reduced FC-SC coupling flexibility in this particular phase. Copyright © 2015 Elsevier B.V. All rights reserved.

Band structure dynamics in indium wires

NASA Astrophysics Data System (ADS)

Chávez-Cervantes, M.; Krause, R.; Aeschlimann, S.; Gierz, I.

2018-05-01

One-dimensional indium wires grown on Si(111) substrates, which are metallic at high temperatures, become insulating below ˜100 K due to the formation of a charge density wave (CDW). The physics of this transition is not conventional and involves a multiband Peierls instability with strong interband coupling. This CDW ground state is readily destroyed with femtosecond laser pulses resulting in a light-induced insulator-to-metal phase transition. The current understanding of this transition remains incomplete, requiring measurements of the transient electronic structure to complement previous investigations of the lattice dynamics. Time- and angle-resolved photoemission spectroscopy with extreme ultraviolet radiation is applied to this end. We find that the transition from the insulating to the metallic band structure occurs within ˜660 fs, which is a fraction of the amplitude mode period. The long lifetime of the transient state (>100 ps) is attributed to trapping in a metastable state in accordance with previous work.

Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S1 states

NASA Astrophysics Data System (ADS)

Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Cabellos, José Luis; Yi, John T.; Pratt, David W.; Schmitt, Michael; Merino, Gabriel; Álvarez-Valtierra, Leonardo

2015-09-01

The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, but it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent -OH and -OCH3 groups plays a major role in these dynamics.

Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S1 states.

PubMed

Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Cabellos, José Luis; Yi, John T; Pratt, David W; Schmitt, Michael; Merino, Gabriel; Álvarez-Valtierra, Leonardo

2015-09-07

The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, but it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent   -OH and   -OCH3 groups plays a major role in these dynamics.

Head-on collision of multistate ultralight BEC dark matter configurations

NASA Astrophysics Data System (ADS)

Guzmán, F. S.; Avilez, Ana A.

2018-06-01

Density profiles of ultralight Bose-condensate dark matter inferred from numerical simulations of structure formation, ruled by the Gross-Pitaevskii-Poisson (GPP) system of equations, have a core-tail structure. Multistate equilibrium configurations of the GPP system, on the other hand, have a similar core-tail density profile. We now submit these multistate configurations to highly dynamical scenarios and show their potential as providers of appropriate density profiles of structures. We present the simulation of head-on collisions between two equilibrium configurations of the GPP system of equations, including the collision of ground state with multistate configurations. We study the regimes of solitonic and merger behavior and show generic properties of the dynamics of the system, including the relaxation process and attractor density profiles. We show that the merger of multistate configurations has the potential to produce core-tail density profiles, with the core dominated by the ground state and the halo dominated by an additional state.

Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

PubMed

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K; Al-Hashimi, Hashim M

2017-05-19

In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

PubMed Central

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K.

2017-01-01

Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. PMID:28369571

Electronic and Structural Elements That Regulate the Excited-State Dynamics in Purine Nucleobase Derivatives

PubMed Central

2015-01-01

The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited 1nπ* state. Following vibrational and conformational relaxation, the 1nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the 1nπ* state while simultaneously facilitating access to the 1ππ*(La)/S0 conical intersection, such that population of the 1nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position. PMID:25763596

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

NASA Astrophysics Data System (ADS)

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-01

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics.

PubMed

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-14

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

A new twist in the photophysics of the GFP chromophore: a volume-conserving molecular torsion couple† †Electronic supplementary information (ESI) available: Synthetic methods and characterization; fluorescence up-conversion data; additional computational details; Cartesian coordinates of key structures; photochemical isomerization data; data for the anion of I. See DOI: 10.1039/c7sc04091a

PubMed Central

Conyard, Jamie; Heisler, Ismael A.; Chan, Yohan; Bulman Page, Philip C.

2018-01-01

The simple structure of the chromophore of the green fluorescent protein (GFP), a phenol and an imidazolone ring linked by a methyne bridge, supports an exceptionally diverse range of excited state phenomena. Here we describe experimentally and theoretically the photochemistry of a novel sterically crowded nonplanar derivative of the GFP chromophore. It undergoes an excited state isomerization reaction accompanied by an exceptionally fast (sub 100 fs) excited state decay. The decay dynamics are essentially independent of solvent polarity and viscosity. Excited state structural dynamics are probed by high level quantum chemical calculations revealing that the fast decay is due to a conical intersection characterized by a twist of the rings and pyramidalization of the methyne bridge carbon. The intersection can be accessed without a barrier from the pre-twisted Franck–Condon structure, and the lack of viscosity dependence is due to the fact that the rings twist in the same direction, giving rise to a volume-conserving decay coordinate. Moreover, the rotation of the phenyl, methyl and imidazolone groups is coupled in the sterically crowded structure, with the methyl group translating the rotation of one ring to the next. As a consequence, the excited state dynamics can be viewed as a torsional couple, where the absorbed photon energy leads to conversion of the out-of-plane orientation from one ring to the other in a volume conserving fashion. A similar modification of the range of methyne dyes may provide a new family of devices for molecular machines, specifically torsional couples. PMID:29675225

Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR.

PubMed

Walinda, Erik; Morimoto, Daichi; Sugase, Kenji

2018-04-26

Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics on the micro- to millisecond timescale. Key biological processes that occur on this timescale include enzymatic catalysis, ligand binding, and local folding. In other words, relaxation-dispersion-resolved dynamics are often closely related to the function of the molecule and therefore highly interesting to the structural biochemist. With an astounding sensitivity of ∼0.5%, the method detects low-population excited states that are invisible to any other biophysical method. The kinetics of the exchange between the ground state and excited states are quantified in the form of the underlying exchange rate, while structural information about the invisible excited state is obtained in the form of its chemical shift. Lastly, the population of the excited state can be derived. This diversity in the information that can be obtained makes relaxation dispersion an excellent method to study the detailed mechanisms of conformational transitions and molecular interactions. Here we describe the two branches of relaxation dispersion, R 2 and R 1ρ , discussing their applicability, similarities, and differences, as well as recent developments in pulse sequence design and data processing. Copyright © 2018 Elsevier Inc. All rights reserved.

Electronic-structure theory of plutonium chalcogenides

NASA Astrophysics Data System (ADS)

Shick, Alexander; Havela, Ladislav; Gouder, Thomas; Rebizant, Jean

2009-03-01

The correlated band theory methods, the around-mean-field LDA + U and dynamical LDA + HIA (Hubbard-I), are applied to investigate the electronic structure of Pu chalcogenides. The LDA + U calculations for PuX (X = S, Se, Te) provide non-magnetic ground state in agreement with the experimental data. Non-integer filling of 5 f-manifold (from approx. 5.6 in PuS to 5.7 PuTe). indicates a mixed valence ground state which combines f5 and f6 multiplets. Making use of the dynamical LDA+HIA method the photoelectron spectra are calculated in good agreement with experimental data. The three-peak feature near EF attributed to 5 f-manifold is well reproduced by LDA + HIA, and follows from mixed valence character of the ground state.

Dynamical networks with topological self-organization

NASA Technical Reports Server (NTRS)

Zak, M.

2001-01-01

Coupled evolution of state and topology of dynamical networks is introduced. Due to the well organized tensor structure, the governing equations are presented in a canonical form, and required attractors as well as their basins can be easily implanted and controlled.

New multirate sampled-data control law structure and synthesis algorithm

NASA Technical Reports Server (NTRS)

Berg, Martin C.; Mason, Gregory S.; Yang, Gen-Sheng

1992-01-01

A new multirate sampled-data control law structure is defined and a new parameter-optimization-based synthesis algorithm for that structure is introduced. The synthesis algorithm can be applied to multirate, multiple-input/multiple-output, sampled-data control laws having a prescribed dynamic order and structure, and a priori specified sampling/update rates for all sensors, processor states, and control inputs. The synthesis algorithm is applied to design two-input, two-output tip position controllers of various dynamic orders for a sixth-order, two-link robot arm model.

Dynamics of SARS-coronavirus HR2 domain in the prefusion and transition states

NASA Astrophysics Data System (ADS)

McReynolds, Susanna; Jiang, Shaokai; Rong, Lijun; Caffrey, Michael

2009-12-01

The envelope glycoproteins S1 and S2 of severe acute respiratory syndrome coronavirus (SARS-CoV) mediate viral entry by conformational change from a prefusion state to a postfusion state that enables fusion of the viral and target membranes. In this work we present the characterization of the dynamic properties of the SARS-CoV S2-HR2 domain (residues 1141-1193 of S) in the prefusion and newly discovered transition states by NMR 15N relaxation studies. The dynamic properties of the different states, which are stabilized under different experimental conditions, extend the current model of viral membrane fusion and give insight into the design of structure-based antagonists of SARS-CoV in particular, as well as other enveloped viruses such as HIV.

Adaptive Sliding Mode Control of Dynamic Systems Using Double Loop Recurrent Neural Network Structure.

PubMed

Fei, Juntao; Lu, Cheng

2018-04-01

In this paper, an adaptive sliding mode control system using a double loop recurrent neural network (DLRNN) structure is proposed for a class of nonlinear dynamic systems. A new three-layer RNN is proposed to approximate unknown dynamics with two different kinds of feedback loops where the firing weights and output signal calculated in the last step are stored and used as the feedback signals in each feedback loop. Since the new structure has combined the advantages of internal feedback NN and external feedback NN, it can acquire the internal state information while the output signal is also captured, thus the new designed DLRNN can achieve better approximation performance compared with the regular NNs without feedback loops or the regular RNNs with a single feedback loop. The new proposed DLRNN structure is employed in an equivalent controller to approximate the unknown nonlinear system dynamics, and the parameters of the DLRNN are updated online by adaptive laws to get favorable approximation performance. To investigate the effectiveness of the proposed controller, the designed adaptive sliding mode controller with the DLRNN is applied to a -axis microelectromechanical system gyroscope to control the vibrating dynamics of the proof mass. Simulation results demonstrate that the proposed methodology can achieve good tracking property, and the comparisons of the approximation performance between radial basis function NN, RNN, and DLRNN show that the DLRNN can accurately estimate the unknown dynamics with a fast speed while the internal states of DLRNN are more stable.

Push or Pull? -- Cryo-Electron Microscopy of Microtubule's Dynamic Instability and Its Roles in the Kinetochore

NASA Astrophysics Data System (ADS)

Wang, Hong-Wei

2009-03-01

Microtubule is a biopolymer made up of alpha-beta-tubulin heterodimers. The tubulin dimers assemble head-to-tail as protofilaments and about 13 protofilaments interact laterally to form a hollow cylindrical structure which is the microtubule. As the major cytoskeleton in all eukaryotic cells, microtubules have the intrinsic property to switch stochastically between growth and shrinkage phases, a phenomenon termed as their dynamic instability. Microtubule's dynamic instability is closely related to the types of nucleotide (GTP or GDP) that binds to the beta-tubulin. We have biochemically trapped two types of assembly states of tubulin with GTP or GDP bound representing the polymerizing and depolymerizing ends of microtubules respectively. Using cryo-electron microscopy, we have elucidated the structures of these intermediate assemblies, showing that tubulin protofilaments demonstrate various curvatures and form different types of lateral interactions depending on the nucleotide states of tubulin and the temperature. Our work indicates that during the microtubule's dynamic cycle, tubulin undergoes various assembly states. These states, different from the straight microtubule, lend the highly dynamic and complicated behavior of microtubules. Our study of microtubule's interaction with certain kinetochore complexes suggests that the intermediate assemblies are responsible for specific mechanical forces that are required during the mitosis or meiosis. Our discoveries strongly suggest that a microtubule is a molecular machine rather than a simple cellular scaffold.

Earth observing satellite: Understanding the Earth as a system

NASA Technical Reports Server (NTRS)

Soffen, Gerald

1990-01-01

There is now a plan for global studies which include two very large efforts. One is the International Geosphere/Biosphere Program (IGBP) sponsored by the International Council of Scientific Unions. The other initiative is Mission to Planet Earth, an unbrella program for doing three kinds of space missions. The major one is the Earth Observation Satellite (EOS). EOS is large polar orbiting satellites with heavy payloads. Two will be placed in orbit by NASA, one by the Japanese and one or two by ESA. The overall mission measurement objectives of EOS are summarized: (1) the global distribution of energy input to and energy output from the Earth; (2) the structure, state variables, composition, and dynamics of the atmosphere from the ground to the mesopause; (3) the physical and biological structure, state, composition, and dynamics of the land surface, including terrestrial and inland water ecosystems; (4) the rates, important sources and sinks, and key components and processes of the Earth's biogeochemical cycles; (5) the circulation, surface temperature, wind stress, sea state, and the biological activity of the oceans; (6) the extent, type, state, elevation, roughness, and dynamics of glaciers, ice sheets, snow and sea ice, and the liquid equivalent of snow in the global cryosphere; (7) the global rates, amounts, and distribution of precipitation; and (8) the dynamic motions of the Earth (geophysics) as a whole, including both rotational dynamics and the kinematic motions of the tectonic plates.

A Deep-Structured Conditional Random Field Model for Object Silhouette Tracking

PubMed Central

Shafiee, Mohammad Javad; Azimifar, Zohreh; Wong, Alexander

2015-01-01

In this work, we introduce a deep-structured conditional random field (DS-CRF) model for the purpose of state-based object silhouette tracking. The proposed DS-CRF model consists of a series of state layers, where each state layer spatially characterizes the object silhouette at a particular point in time. The interactions between adjacent state layers are established by inter-layer connectivity dynamically determined based on inter-frame optical flow. By incorporate both spatial and temporal context in a dynamic fashion within such a deep-structured probabilistic graphical model, the proposed DS-CRF model allows us to develop a framework that can accurately and efficiently track object silhouettes that can change greatly over time, as well as under different situations such as occlusion and multiple targets within the scene. Experiment results using video surveillance datasets containing different scenarios such as occlusion and multiple targets showed that the proposed DS-CRF approach provides strong object silhouette tracking performance when compared to baseline methods such as mean-shift tracking, as well as state-of-the-art methods such as context tracking and boosted particle filtering. PMID:26313943

Competitive Dynamics on Complex Networks

PubMed Central

Zhao, Jiuhua; Liu, Qipeng; Wang, Xiaofan

2014-01-01

We consider a dynamical network model in which two competitors have fixed and different states, and each normal agent adjusts its state according to a distributed consensus protocol. The state of each normal agent converges to a steady value which is a convex combination of the competitors' states, and is independent of the initial states of agents. This implies that the competition result is fully determined by the network structure and positions of competitors in the network. We compute an Influence Matrix (IM) in which each element characterizing the influence of an agent on another agent in the network. We use the IM to predict the bias of each normal agent and thus predict which competitor will win. Furthermore, we compare the IM criterion with seven node centrality measures to predict the winner. We find that the competitor with higher Katz Centrality in an undirected network or higher PageRank in a directed network is most likely to be the winner. These findings may shed new light on the role of network structure in competition and to what extent could competitors adjust network structure so as to win the competition. PMID:25068622

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Li, Kun; Drobny, Gary P.; Castner, David G.

2010-01-01

The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately. PMID:20628016

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

PubMed Central

van den Bedem, Henry; Fraser, James S.

2015-01-01

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

Quantum trajectory phase transitions in the micromaser.

PubMed

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.

Instantaneous brain dynamics mapped to a continuous state space.

PubMed

Billings, Jacob C W; Medda, Alessio; Shakil, Sadia; Shen, Xiaohong; Kashyap, Amrit; Chen, Shiyang; Abbas, Anzar; Zhang, Xiaodi; Nezafati, Maysam; Pan, Wen-Ju; Berman, Gordon J; Keilholz, Shella D

2017-11-15

Measures of whole-brain activity, from techniques such as functional Magnetic Resonance Imaging, provide a means to observe the brain's dynamical operations. However, interpretation of whole-brain dynamics has been stymied by the inherently high-dimensional structure of brain activity. The present research addresses this challenge through a series of scale transformations in the spectral, spatial, and relational domains. Instantaneous multispectral dynamics are first developed from input data via a wavelet filter bank. Voxel-level signals are then projected onto a representative set of spatially independent components. The correlation distance over the instantaneous wavelet-ICA state vectors is a graph that may be embedded onto a lower-dimensional space to assist the interpretation of state-space dynamics. Applying this procedure to a large sample of resting-state and task-active data (acquired through the Human Connectome Project), we segment the empirical state space into a continuum of stimulus-dependent brain states. Upon observing the local neighborhood of brain-states adopted subsequent to each stimulus, we may conclude that resting brain activity includes brain states that are, at times, similar to those adopted during tasks, but that are at other times distinct from task-active brain states. As task-active brain states often populate a local neighborhood, back-projection of segments of the dynamical state space onto the brain's surface reveals the patterns of brain activity that support many experimentally-defined states. Copyright © 2017 Elsevier Inc. All rights reserved.

Models of charge pair generation in organic solar cells.

PubMed

Few, Sheridan; Frost, Jarvist M; Nelson, Jenny

2015-01-28

Efficient charge pair generation is observed in many organic photovoltaic (OPV) heterojunctions, despite nominal electron-hole binding energies which greatly exceed the average thermal energy. Empirically, the efficiency of this process appears to be related to the choice of donor and acceptor materials, the resulting sequence of excited state energy levels and the structure of the interface. In order to establish a suitable physical model for the process, a range of different theoretical studies have addressed the nature and energies of the interfacial states, the energetic profile close to the heterojunction and the dynamics of excited state transitions. In this paper, we review recent developments underpinning the theory of charge pair generation and phenomena, focussing on electronic structure calculations, electrostatic models and approaches to excited state dynamics. We discuss the remaining challenges in achieving a predictive approach to charge generation efficiency.

Performance of Koyna dam based on static and dynamic analysis

NASA Astrophysics Data System (ADS)

Azizan, Nik Zainab Nik; Majid, Taksiah A.; Nazri, Fadzli Mohamed; Maity, Damodar

2017-10-01

This paper discusses the performance of Koyna dam based on static pushover analysis (SPO) and incremental dynamic analysis (IDA). The SPO in this study considered two type of lateral load which is inertial load and hydrodynamic load. The structure was analyse until the damage appears on the structure body. The IDA curves were develop based on 7 ground motion, where the characteristic of the ground motions: i) the distance from the epicenter is less than 15km, (ii) the magnitude is equal to or greater than 5.5 and (iii) the PGA is equal to or greater than 0.15g. All the ground motions convert to respond spectrum and scaled according to the developed elastic respond spectrum in order to match the characteristic of the ground motion to the soil type. Elastic respond spectrum developed based on soil type B by using Eurocode 8. By using SPO and IDA method are able to determine the limit states of the dam. The limit state proposed in this study are yielding and ultimate state which is identified base on crack pattern perform on the structure model. The comparison of maximum crest displacement for both methods is analysed to define the limit state of the dam. The displacement of yielding state for Koyna dam is 23.84mm and 44.91mm for the ultimate state. The results are able to be used as a guideline to monitor Koyna dam under seismic loadings which are considering static and dynamic.

G-quadruplex dynamics.

PubMed

Harkness, Robert W; Mittermaier, Anthony K

2017-11-01

G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations. The impact of these dynamics on biological function is currently not well understood. Recently, structural dynamics have been demonstrated to entropically stabilize GQ ensembles, potentially modulating gene expression. Transient, low-populated states in GQ ensembles may additionally regulate nucleic acid interactions and function. This review will underscore the interplay of GQ dynamics and biological function, focusing on several dynamic processes for biological GQs and the characterization of GQ dynamics by nuclear magnetic resonance (NMR) spectroscopy in conjunction with other biophysical techniques. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Overlapping community detection based on link graph using distance dynamics

NASA Astrophysics Data System (ADS)

Chen, Lei; Zhang, Jing; Cai, Li-Jun

2018-01-01

The distance dynamics model was recently proposed to detect the disjoint community of a complex network. To identify the overlapping structure of a network using the distance dynamics model, an overlapping community detection algorithm, called L-Attractor, is proposed in this paper. The process of L-Attractor mainly consists of three phases. In the first phase, L-Attractor transforms the original graph to a link graph (a new edge graph) to assure that one node has multiple distances. In the second phase, using the improved distance dynamics model, a dynamic interaction process is introduced to simulate the distance dynamics (shrink or stretch). Through the dynamic interaction process, all distances converge, and the disjoint community structure of the link graph naturally manifests itself. In the third phase, a recovery method is designed to convert the disjoint community structure of the link graph to the overlapping community structure of the original graph. Extensive experiments are conducted on the LFR benchmark networks as well as real-world networks. Based on the results, our algorithm demonstrates higher accuracy and quality than other state-of-the-art algorithms.

Stress state reassessment of Romanian offshore structures taking into account corrosion influence

NASA Astrophysics Data System (ADS)

Joavină, R.; Zăgan, S.; Zăgan, R.; Popa, M.

2017-08-01

Progressive degradation analysis for extraction or exploration offshore structure, with appraisal of failure potential and the causes that can be correlated with the service age, depends on the various sources of uncertainty that require particular attention in design, construction and exploitation phases. Romanian self erecting platforms are spatial lattice structures consist of tubular steel joints, forming a continuous system with an infinite number of dynamic degrees of freedom. Reassessment of a structure at fixed intervals of time, recorrelation of initial design elements with the actual situation encountered in location and with structural behaviour represents a major asset in lowering vulnerabilities of offshore structure. This paper proposes a comparative reassessment of the stress state for an offshore structure Gloria type, when leaving the shipyard and at the end of that interval corresponding to capital revision, taking into account sectional changes due to marine environment corrosion. The calculation was done using Newmark integration method on a 3D model, asses of the dynamic loads was made through probabilistic spectral method.

Steady state solutions to dynamically loaded periodic structures

NASA Technical Reports Server (NTRS)

Kalinowski, A. J.

1980-01-01

The general problem of solving for the steady state (time domain) dynamic response (i.e., NASTRAN rigid format-8) of a general elastic periodic structure subject to a phase difference loading of the type encountered in traveling wave propagation problems was studied. Two types of structural configurations were considered; in the first type, the structure has a repeating pattern over a span that is long enough to be considered, for all practical purposes, as infinite; in the second type, the structure has structural rotational symmetry in the circumferential direction. The theory and a corresponding set of DMAP instructions which permits the NASTRAN user to automatically alter the rigid format-8 sequence to solve the intended class of problems are presented. Final results are recovered as with any ordinary rigid format-8 solution, except that the results are only printed for the typical periodic segment of the structure. A simple demonstration problem having a known exact solution is used to illustrate the implementation of the procedure.

Discovering Coherent Structures Using Local Causal States

NASA Astrophysics Data System (ADS)

Rupe, Adam; Crutchfield, James P.; Kashinath, Karthik; Prabhat, Mr.

2017-11-01

Coherent structures were introduced in the study of fluid dynamics and were initially defined as regions characterized by high levels of coherent vorticity, i.e. regions where instantaneously space and phase correlated vorticity are high. In a more general spatiotemporal setting, coherent structures can be seen as localized broken symmetries which persist in time. Building off the computational mechanics framework, which integrates tools from computation and information theory to capture pattern and structure in nonlinear dynamical systems, we introduce a theory of coherent structures, in the more general sense. Central to computational mechanics is the causal equivalence relation, and a local spatiotemporal generalization of it is used to construct the local causal states, which are utilized to uncover a system's spatiotemporal symmetries. Coherent structures are then identified as persistent, localized deviations from these symmetries. We illustrate how novel patterns and structures can be discovered in cellular automata and outline the path from them to laminar, transitional and turbulent flows. Funded by Intel through the Big Data Center at LBNL and the IPCC at UC Davis.

Testing of Composite Fan Vanes With Erosion-Resistant Coating Accelerated

NASA Technical Reports Server (NTRS)

Bowman, Cheryl L.; Sutter, James K.; Otten, Kim D.; Samorezov, Sergey; Perusek, Gail P.

2004-01-01

The high-cycle fatigue of composite stator vanes provided an accelerated life-state prior to insertion in a test stand engine. The accelerated testing was performed in the Structural Dynamics Laboratory at the NASA Glenn Research Center under the guidance of Structural Mechanics and Dynamics Branch personnel. Previous research on fixturing and test procedures developed at Glenn determined that engine vibratory conditions could be simulated for polymer matrix composite vanes by using the excitation of a combined slip table and electrodynamic shaker in Glenn's Structural Dynamics Laboratory. Bench-top testing gave researchers the confidence to test the coated vanes in a full-scale engine test.

Dynamically tunable interface states in 1D graphene-embedded photonic crystal heterostructure

NASA Astrophysics Data System (ADS)

Huang, Zhao; Li, Shuaifeng; Liu, Xin; Zhao, Degang; Ye, Lei; Zhu, Xuefeng; Zang, Jianfeng

2018-03-01

Optical interface states exhibit promising applications in nonlinear photonics, low-threshold lasing, and surface-wave assisted sensing. However, the further application of interface states in configurable optics is hindered by their limited tunability. Here, we demonstrate a new approach to generate dynamically tunable and angle-resolved interface states using graphene-embedded photonic crystal (GPC) heterostructure device. By combining the GPC structure design with in situ electric doping of graphene, a continuously tunable interface state can be obtained and its tuning range is as wide as the full bandgap. Moreover, the exhibited tunable interface states offer a possibility to study the correspondence between space and time characteristics of light, which is beyond normal incident conditions. Our strategy provides a new way to design configurable devices with tunable optical states for various advanced optical applications such as beam splitter and dynamically tunable laser.

Structure of bicomponent particles synthesized from colliding metal clusters

NASA Astrophysics Data System (ADS)

Kryzhevich, D. S.; Zolnikov, K. P.; Korchuganov, A. V.; Psakhie, S. G.

2017-12-01

Here, based on a molecular dynamics simulation with many-body interaction potentials, we consider several scenarios of the formation of bicomponent particles from colliding clusters in an electrical explosion of Cu and Ni wires. The data suggest that the structure of bicomponent particles depends largely on the explosion time of one wire with respect to the other and on the phase state of colliding clusters. Diagrams are presented demonstrating the dynamics of bicomponent particles with block structure synthesized from crystalline Ni and molten Cu clusters.

Structure of a viscoplastic theory

NASA Technical Reports Server (NTRS)

Freed, Alan D.

1988-01-01

The general structure of a viscoplastic theory is developed from physical and thermodynamical considerations. The flow equation is of classical form. The dynamic recovery approach is shown to be superior to the hardening function approach for incorporating nonlinear strain hardening into the material response through the evolutionary equation for back stress. A novel approach for introducing isotropic strain hardening into the theory is presented, which results in a useful simplification. In particular, the limiting stress for the kinematic saturation of state (not the drag stress) is the chosen scalar-valued state variable. The resulting simplification is that there is no coupling between dynamic and thermal recovery terms in each evolutionary equation. The derived theory of viscoplasticity has the structure of a two-surface plasticity theory when the response is plasticlike, and the structure of a Bailey-Orowan creep theory when the response is creeplike.

Atomic-level structure characterization of biomass pre- and post-lignin treatment by dynamic nuclear polarization-enhanced solid-state NMR

DOE PAGES

Perras, Frederic A.; Luo, Hao; Zhang, Ximing; ...

2016-12-27

Here, lignocellulosic biomass is a promising sustainable feedstock for the production of biofuels, biomaterials, and biospecialty chemicals. However, efficient utilization of biomass has been limited by our poor understanding of its molecular structure. Here, we report a dynamic nuclear polarization (DNP)-enhanced solid-state (SS)NMR study of the molecular structure of biomass, both pre- and postcatalytic treatment. This technique enables the measurement of 2D homonuclear 13C– 13C correlation SSNMR spectra under natural abundance, yielding, for the first time, an atomic-level picture of the structure of raw and catalytically treated biomass samples. We foresee that further such experiments could be used to determinemore » structure–function relationships and facilitate the development of more efficient, and chemically targeted, biomass-conversion technologies.« less

Atomic-level structure characterization of biomass pre- and post-lignin treatment by dynamic nuclear polarization-enhanced solid-state NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perras, Frederic A.; Luo, Hao; Zhang, Ximing

Here, lignocellulosic biomass is a promising sustainable feedstock for the production of biofuels, biomaterials, and biospecialty chemicals. However, efficient utilization of biomass has been limited by our poor understanding of its molecular structure. Here, we report a dynamic nuclear polarization (DNP)-enhanced solid-state (SS)NMR study of the molecular structure of biomass, both pre- and postcatalytic treatment. This technique enables the measurement of 2D homonuclear 13C– 13C correlation SSNMR spectra under natural abundance, yielding, for the first time, an atomic-level picture of the structure of raw and catalytically treated biomass samples. We foresee that further such experiments could be used to determinemore » structure–function relationships and facilitate the development of more efficient, and chemically targeted, biomass-conversion technologies.« less

Minimal complexity control law synthesis

NASA Technical Reports Server (NTRS)

Bernstein, Dennis S.; Haddad, Wassim M.; Nett, Carl N.

1989-01-01

A paradigm for control law design for modern engineering systems is proposed: Minimize control law complexity subject to the achievement of a specified accuracy in the face of a specified level of uncertainty. Correspondingly, the overall goal is to make progress towards the development of a control law design methodology which supports this paradigm. Researchers achieve this goal by developing a general theory of optimal constrained-structure dynamic output feedback compensation, where here constrained-structure means that the dynamic-structure (e.g., dynamic order, pole locations, zero locations, etc.) of the output feedback compensation is constrained in some way. By applying this theory in an innovative fashion, where here the indicated iteration occurs over the choice of the compensator dynamic-structure, the paradigm stated above can, in principle, be realized. The optimal constrained-structure dynamic output feedback problem is formulated in general terms. An elegant method for reducing optimal constrained-structure dynamic output feedback problems to optimal static output feedback problems is then developed. This reduction procedure makes use of star products, linear fractional transformations, and linear fractional decompositions, and yields as a byproduct a complete characterization of the class of optimal constrained-structure dynamic output feedback problems which can be reduced to optimal static output feedback problems. Issues such as operational/physical constraints, operating-point variations, and processor throughput/memory limitations are considered, and it is shown how anti-windup/bumpless transfer, gain-scheduling, and digital processor implementation can be facilitated by constraining the controller dynamic-structure in an appropriate fashion.

Dynamics of influence on hierarchical structures

NASA Astrophysics Data System (ADS)

Fotouhi, Babak; Rabbat, Michael G.

2013-08-01

Dichotomous spin dynamics on a pyramidal hierarchical structure (the Bethe lattice) are studied. The system embodies a number of classes, where a class comprises nodes that are equidistant from the root (head node). Weighted links exist between nodes from the same and different classes. The spin (hereafter state) of the head node is fixed. We solve for the dynamics of the system for different boundary conditions. We find necessary conditions so that the classes eventually repudiate or acquiesce in the state imposed by the head node. The results indicate that to reach unanimity across the hierarchy, it suffices that the bottommost class adopts the same state as the head node. Then the rest of the hierarchy will inevitably comply. This also sheds light on the importance of mass media as a means of synchronization between the topmost and bottommost classes. Surprisingly, in the case of discord between the head node and the bottommost classes, the average state over all nodes inclines towards that of the bottommost class regardless of the link weights and intraclass configurations. Hence the role of the bottommost class is signified.

Controlling the excited-state dynamics of low band gap, near-infrared absorbers via proquinoidal unit electronic structural modulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Yusong; Rawson, Jeff; Roget, Sean A.

While the influence of proquinoidal character upon the linear absorption spectrum of low optical bandgap π-conjugated polymers and molecules is well understood, its impact upon excited-state relaxation pathways and dynamics remains obscure. We report the syntheses, electronic structural properties, and excited-state dynamics of a series of model highly conjugated near-infrared (NIR)-absorbing chromophores based on a (porphinato)metal(II)-proquinoidal spacer-(porphinato)metal(II) (PM-Sp-PM) structural motif. A combination of excited-state dynamical studies and time-dependent density functional theory calculations: (i) points to the cardinal role that excited-state configuration interaction (CI) plays in determining the magnitudes of S 1 → S 0 radiative (k r), S 1 → T 1 intersystem crossing (k ISC), and S 1 → S 0 internal conversion (k IC) rate constants in these PM-Sp-PM chromophores, and (ii) suggests that a primary determinant of CI magnitude derives from the energetic alignment of the PM and Sp fragment LUMOs (ΔE L). These insights not only enable steering of excited-state relaxation dynamics of high oscillator strength NIR absorbers to realize either substantial fluorescence or long-lived triplets (τmore » $$_ {T_1}$$ > μs) generated at unit quantum yield (Φ ISC = 100%), but also crafting of those having counter-intuitive properties: for example, while (porphinato)platinum compounds are well known to generate non-emissive triplet states (Φ ISC = 100%) upon optical excitation at ambient temperature, diminishing the extent of excited-state CI in these systems realizes long-wavelength absorbing heavy-metal fluorophores. In conclusion, this work highlights approaches to: (i) modulate low-lying singlet excited-state lifetime over the picosecond-to-nanosecond time domain, (ii) achieve NIR fluorescence with quantum yields up to 25%, (iii) tune the magnitude of S 1–T 1 ISC rate constant from 10 9 to 10 12 s -1 and (iv) realize T 1-state lifetimes that range from ~0.1 to several μs, for these model PM-Sp-PM chromophores, and renders new insights to evolve bespoke photophysical properties for low optical bandgap π-conjugated polymers and molecules based on proquinoidal conjugation motifs.« less

Controlling the excited-state dynamics of low band gap, near-infrared absorbers via proquinoidal unit electronic structural modulation

DOE PAGES

Bai, Yusong; Rawson, Jeff; Roget, Sean A.; ...

2017-06-07

While the influence of proquinoidal character upon the linear absorption spectrum of low optical bandgap π-conjugated polymers and molecules is well understood, its impact upon excited-state relaxation pathways and dynamics remains obscure. We report the syntheses, electronic structural properties, and excited-state dynamics of a series of model highly conjugated near-infrared (NIR)-absorbing chromophores based on a (porphinato)metal(II)-proquinoidal spacer-(porphinato)metal(II) (PM-Sp-PM) structural motif. A combination of excited-state dynamical studies and time-dependent density functional theory calculations: (i) points to the cardinal role that excited-state configuration interaction (CI) plays in determining the magnitudes of S 1 → S 0 radiative (k r), S 1 → T 1 intersystem crossing (k ISC), and S 1 → S 0 internal conversion (k IC) rate constants in these PM-Sp-PM chromophores, and (ii) suggests that a primary determinant of CI magnitude derives from the energetic alignment of the PM and Sp fragment LUMOs (ΔE L). These insights not only enable steering of excited-state relaxation dynamics of high oscillator strength NIR absorbers to realize either substantial fluorescence or long-lived triplets (τmore » $$_ {T_1}$$ > μs) generated at unit quantum yield (Φ ISC = 100%), but also crafting of those having counter-intuitive properties: for example, while (porphinato)platinum compounds are well known to generate non-emissive triplet states (Φ ISC = 100%) upon optical excitation at ambient temperature, diminishing the extent of excited-state CI in these systems realizes long-wavelength absorbing heavy-metal fluorophores. In conclusion, this work highlights approaches to: (i) modulate low-lying singlet excited-state lifetime over the picosecond-to-nanosecond time domain, (ii) achieve NIR fluorescence with quantum yields up to 25%, (iii) tune the magnitude of S 1–T 1 ISC rate constant from 10 9 to 10 12 s -1 and (iv) realize T 1-state lifetimes that range from ~0.1 to several μs, for these model PM-Sp-PM chromophores, and renders new insights to evolve bespoke photophysical properties for low optical bandgap π-conjugated polymers and molecules based on proquinoidal conjugation motifs.« less

Synchronization in dynamical networks with unconstrained structure switching

NASA Astrophysics Data System (ADS)

del Genio, Charo I.; Romance, Miguel; Criado, Regino; Boccaletti, Stefano

2015-12-01

We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the structure is determined indirectly from a carefully built transformation of the eigenvector matrices of the coupling Laplacians, which are guaranteed to change smoothly in time. In turn, this allows one to extend the master stability function formalism, which can be used to assess the stability of a synchronized state. This approach is independent from the particular topologies that the network visits, and is not restricted to commuting structures. Also, it does not depend on the time scale of the evolution, which can be faster than, comparable to, or even secular with respect to the dynamics of the units.

X-ray Scattering Combined with Coordinate-Based Analyses for Applications in Natural and Artificial Photosynthesis

PubMed Central

Tiede, David M.; Mardis, Kristy L.; Zuo, Xiaobing

2009-01-01

Advances in x-ray light sources and detectors have created opportunities for advancing our understanding of structure and structural dynamics for supramolecular assemblies in solution by combining x-ray scattering measurement with coordinate-based modeling methods. In this review the foundations for x-ray scattering are discussed and illustrated with selected examples demonstrating the ability to correlate solution x-ray scattering measurements to molecular structure, conformation, and dynamics. These approaches are anticipated to have a broad range of applications in natural and artificial photosynthesis by offering possibilities for structure resolution for dynamic supramolecular assemblies in solution that can not be fully addressed with crystallographic techniques, and for resolving fundamental mechanisms for solar energy conversion by mapping out structure in light-excited reaction states. PMID:19636808

[Characterization of structural change of ascorbate peroxidase from Chinese kale during denaturation by circular dichroism].

PubMed

Xi, Jia-Fu; Tang, Lei; Zhang, Jian-Hua; Zhang, Hong-Jian; Chen, Xu-Sheng; Mao, Zhong-Gui

2014-11-01

Circular dichroism (CD) is a special absorption spectrum. The secondary structure of protein such as α-helix, β-sheet and β-turn in the far ultraviolet region (190-250 nm) has a characteristic CD spectrum. In order to understand the activity and structural changes of ascorbate peroxidase from Chinese kale (BaAPX) during denaturation, specific activity and percentage of secondary structure of BaAPX under different time, temperature and concentration were analyzed by CD dynamically. In addition, the percentage of four secondary structures in BaAPX was calculated by CD analysis software Dichroweb. The results show that BaAPX is a full α-type enzyme whose specific activity is positively related to the percentage of α-helix. During denaturation of BaAPX, three kinds of structural changes were proposed: the one-step structural change from initial state (N state) to minimum state of α-helix (R state) under low concentration and low temperature; the one-step structural change from N state to equilibrium state (T state) under high concentration and low temperature; the two-step structural changes from N state through R state to final T state under heat treatment and low temperature renaturation.

Real time assessment of dynamic loads on bridges.

DOT National Transportation Integrated Search

2013-05-01

Highway bridges are an important class of civil structures that are subject to continuously : acting and varying dynamic loads due to traffic. A large number of highway bridges in the US : (bridges on interstate highways or state highways which have ...

Understanding ion association states and molecular dynamics using infrared spectroscopy

NASA Astrophysics Data System (ADS)

Masser, Hanqing

A molecular level understanding of the ion transport mechanism within polymer electrolytes is crucial to the further development for advanced energy storage applications. This can be achieved by the identification and quantitative measurement of different ion species in the system and further relating them to the ion conductivity. In the first part of this thesis, research is presented towards understanding the ion association states (free ions, ion pairs and ion aggregates) in ionomer systems, and the correlation of ion association states, ion conduction, polymer dynamics, and morphology. Ion conductivity in ionomers can be improved by lowering glass transition temperature, increasing polymer ion solvation ability, and adjusting ionomer structural variables such as ion content, cation type and side chain structure. These effects are studied in three ionomer systems respectively, using a combination of characterization methods. Fourier Transform Infrared Spectroscopy (FTIR) identifies and quantifies the ion association states. Dielectric Spectroscopy (DRS) characterizes ion conductivity and polymer and ion dynamics. X-ray scattering reveals changes in morphology. The influence of a cation solvating plasticizer on a polyester ionomer is systematically investigated with respect to ion association states, ion and polymer dynamics and morphology. A decrease in the number ratio of ion aggregates with increased plasticizer content and a slight increase at elevated temperature are observed in FTIR. Similar results are also detected by X-ray scattering. As determined from dielectric spectroscopy, ion conductivity increases with plasticizer content, in accordance with the decrease in glass transition temperature. Research on copolymer of poly(ethylene oxide) (PEO) and poly(tetramethylene oxide) (PTMO) based ionomers further develops an understanding of the trade-off between ion solvation and segmental dynamics. Upon the incorporation of PTMO, the majority of the PTMO microphase separates from the PEO-rich microphase, and ionic groups are preferentially solvated by PEO chains and reside in the PEO-rich microphase. As the ratio of PTMO increases, the fraction of aggregates increases, resulting in more highly coordinated aggregation states. Results on ion association states are in good agreement with previous results on ion conductivity, polymer dynamics and morphology. The effects of ion content, cation type and ionic side chain structure on ion association states are systemically studied in a series of ionomers with short ethylene oxide and ionic sulfonated styrene side chains, and then correlated to the ion and polymer dynamic characterization. It is found that ionomers with modest ion content, large cation and styrene ionic side chain have the most "free ions" and ion pairs, and highest ion conductivity. Ion conduction in ionomers is optimized by systematically changing their chemical structures. In addition to knowledge of ion association states, a IR band shape also contains information on molecular dynamics. In companion investigation, the vibrational relaxation and dynamic transitions of conformationally insensitive normal modes in two different polymer systems (atactic polystyrene and deuterated poly(methyl methacrylate)) are studied. The information on vibrational relaxations is resolved by conducting precisely controlled FTIR experiments, applying specialized curve resolving data analysis, and calculating time correlation functions through numerical Fourier transformation. The vibrational relaxations of these modes can be described by a two process model: a fast process on the time scale of 0.01 ps, which is inhomogeneously broadened by a slow process on the time scale of picoseconds.

Full-dimensional ground- and excited-state potential energy surfaces and state couplings for photodissociation of thioanisole

NASA Astrophysics Data System (ADS)

Li, Shaohong L.; Truhlar, Donald G.

2017-02-01

Analytic potential energy surfaces (PESs) and state couplings of the ground and two lowest singlet excited states of thioanisole (C6H5SCH3) are constructed in a diabatic representation based on electronic structure calculations including dynamic correlation. They cover all 42 internal degrees of freedom and a wide range of geometries including the Franck-Condon region and the reaction valley along the breaking S-CH3 bond with the full ranges of the torsion angles. The parameters in the PESs and couplings are fitted to the results of smooth diabatic electronic structure calculations including dynamic electron correlation by the extended multi-configurational quasi-degenerate perturbation theory method for the adiabatic state energies followed by diabatization by the fourfold way. The fit is accomplished by the anchor points reactive potential method with two reactive coordinates and 40 nonreactive degrees of freedom, where the anchor-point force fields are obtained with a locally modified version of the QuickFF package. The PESs and couplings are suitable for study of the topography of the trilayer potential energy landscape and for electronically nonadiabatic molecular dynamics simulations of the photodissociation of the S-CH3 bond.

Zombie states for description of structure and dynamics of multi-electron systems

NASA Astrophysics Data System (ADS)

Shalashilin, Dmitrii V.

2018-05-01

Canonical Coherent States (CSs) of Harmonic Oscillator have been extensively used as a basis in a number of computational methods of quantum dynamics. However, generalising such techniques for fermionic systems is difficult because Fermionic Coherent States (FCSs) require complicated algebra of Grassmann numbers not well suited for numerical calculations. This paper introduces a coherent antisymmetrised superposition of "dead" and "alive" electronic states called here Zombie State (ZS), which can be used in a manner of FCSs but without Grassmann algebra. Instead, for Zombie States, a very simple sign-changing rule is used in the definition of creation and annihilation operators. Then, calculation of electronic structure Hamiltonian matrix elements between two ZSs becomes very simple and a straightforward technique for time propagation of fermionic wave functions can be developed. By analogy with the existing methods based on Canonical Coherent States of Harmonic Oscillator, fermionic wave functions can be propagated using a set of randomly selected Zombie States as a basis. As a proof of principles, the proposed Coupled Zombie States approach is tested on a simple example showing that the technique is exact.

Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin—Molecular Dynamics Simulations of the Ground State and the M-Intermediate

PubMed Central

Grudinin, Sergei; Büldt, Georg; Gordeliy, Valentin; Baumgaertner, Artur

2005-01-01

Protein crystallography provides the structure of a protein, averaged over all elementary cells during data collection time. Thus, it has only a limited access to diffusive processes. This article demonstrates how molecular dynamics simulations can elucidate structure-function relationships in bacteriorhodopsin (bR) involving water molecules. The spatial distribution of water molecules and their corresponding hydrogen-bonded networks inside bR in its ground state (G) and late M intermediate conformations were investigated by molecular dynamics simulations. The simulations reveal a much higher average number of internal water molecules per monomer (28 in the G and 36 in the M) than observed in crystal structures (18 and 22, respectively). We found nine water molecules trapped and 19 diffusive inside the G-monomer, and 13 trapped and 23 diffusive inside the M-monomer. The exchange of a set of diffusive internal water molecules follows an exponential decay with a 1/e time in the order of 340 ps for the G state and 460 ps for the M state. The average residence time of a diffusive water molecule inside the protein is ∼95 ps for the G state and 110 ps for the M state. We have used the Grotthuss model to describe the possible proton transport through the hydrogen-bonded networks inside the protein, which is built up in the picosecond-to-nanosecond time domains. Comparing the water distribution and hydrogen-bonded networks of the two different states, we suggest possible pathways for proton hopping and water movement inside bR. PMID:15731388

Network structure shapes spontaneous functional connectivity dynamics.

PubMed

Shen, Kelly; Hutchison, R Matthew; Bezgin, Gleb; Everling, Stefan; McIntosh, Anthony R

2015-04-08

The structural organization of the brain constrains the range of interactions between different regions and shapes ongoing information processing. Therefore, it is expected that large-scale dynamic functional connectivity (FC) patterns, a surrogate measure of coordination between brain regions, will be closely tied to the fiber pathways that form the underlying structural network. Here, we empirically examined the influence of network structure on FC dynamics by comparing resting-state FC (rsFC) obtained using BOLD-fMRI in macaques (Macaca fascicularis) to structural connectivity derived from macaque axonal tract tracing studies. Consistent with predictions from simulation studies, the correspondence between rsFC and structural connectivity increased as the sample duration increased. Regions with reciprocal structural connections showed the most stable rsFC across time. The data suggest that the transient nature of FC is in part dependent on direct underlying structural connections, but also that dynamic coordination can occur via polysynaptic pathways. Temporal stability was found to be dependent on structural topology, with functional connections within the rich-club core exhibiting the greatest stability over time. We discuss these findings in light of highly variable functional hubs. The results further elucidate how large-scale dynamic functional coordination exists within a fixed structural architecture. Copyright © 2015 the authors 0270-6474/15/355579-10$15.00/0.

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

DOE PAGES

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

Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation

NASA Astrophysics Data System (ADS)

Mereuta, Loredana; Roy, Mahua; Asandei, Alina; Lee, Jong Kook; Park, Yoonkyung; Andricioaei, Ioan; Luchian, Tudor

2014-01-01

The microscopic details of how peptides translocate one at a time through nanopores are crucial determinants for transport through membrane pores and important in developing nano-technologies. To date, the translocation process has been too fast relative to the resolution of the single molecule techniques that sought to detect its milestones. Using pH-tuned single-molecule electrophysiology and molecular dynamics simulations, we demonstrate how peptide passage through the α-hemolysin protein can be sufficiently slowed down to observe intermediate single-peptide sub-states associated to distinct structural milestones along the pore, and how to control residence time, direction and the sequence of spatio-temporal state-to-state dynamics of a single peptide. Molecular dynamics simulations of peptide translocation reveal the time- dependent ordering of intermediate structures of the translocating peptide inside the pore at atomic resolution. Calculations of the expected current ratios of the different pore-blocking microstates and their time sequencing are in accord with the recorded current traces.

Subtle Monte Carlo Updates in Dense Molecular Systems.

PubMed

Bottaro, Sandro; Boomsma, Wouter; E Johansson, Kristoffer; Andreetta, Christian; Hamelryck, Thomas; Ferkinghoff-Borg, Jesper

2012-02-14

Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.

A systematic review of lumped-parameter equivalent circuit models for real-time estimation of lithium-ion battery states

NASA Astrophysics Data System (ADS)

Nejad, S.; Gladwin, D. T.; Stone, D. A.

2016-06-01

This paper presents a systematic review for the most commonly used lumped-parameter equivalent circuit model structures in lithium-ion battery energy storage applications. These models include the Combined model, Rint model, two hysteresis models, Randles' model, a modified Randles' model and two resistor-capacitor (RC) network models with and without hysteresis included. Two variations of the lithium-ion cell chemistry, namely the lithium-ion iron phosphate (LiFePO4) and lithium nickel-manganese-cobalt oxide (LiNMC) are used for testing purposes. The model parameters and states are recursively estimated using a nonlinear system identification technique based on the dual Extended Kalman Filter (dual-EKF) algorithm. The dynamic performance of the model structures are verified using the results obtained from a self-designed pulsed-current test and an electric vehicle (EV) drive cycle based on the New European Drive Cycle (NEDC) profile over a range of operating temperatures. Analysis on the ten model structures are conducted with respect to state-of-charge (SOC) and state-of-power (SOP) estimation with erroneous initial conditions. Comparatively, both RC model structures provide the best dynamic performance, with an outstanding SOC estimation accuracy. For those cell chemistries with large inherent hysteresis levels (e.g. LiFePO4), the RC model with only one time constant is combined with a dynamic hysteresis model to further enhance the performance of the SOC estimator.

Ultrafast carrier dynamics in a GaN/Al 0.18Ga0.82N superlattice

NASA Astrophysics Data System (ADS)

Mahler, Felix; Tomm, Jens W.; Reimann, Klaus; Woerner, Michael; Elsaesser, Thomas; Flytzanis, Christos; Hoffmann, Veit; Weyers, Markus

2018-04-01

Relaxation processes of photoexcited carriers in a GaN /Al0.18Ga0.82N superlattice are studied in femtosecond spectrally resolved reflectivity measurements at ambient temperature. The transient reflectivity reveals electron trapping into defect states close to the conduction-band minimum with a 150-200 fs time constant, followed by few-picosecond carrier cooling. A second slower trapping process into a different manifold of defect states is observed on a time scale of approximately 10 ps. Our results establish the prominent role of structural defects and disorder for ultrafast carrier dynamics in nitride semiconductor structures.

Structural dynamics of a noncovalent charge transfer complex from femtosecond stimulated Raman spectroscopy.

PubMed

Fujisawa, Tomotsumi; Creelman, Mark; Mathies, Richard A

2012-09-06

Femtosecond stimulated Raman spectroscopy is used to examine the structural dynamics of photoinduced charge transfer within a noncovalent electron acceptor/donor complex of pyromellitic dianhydride (PMDA, electron acceptor) and hexamethylbenzene (HMB, electron donor) in ethylacetate and acetonitrile. The evolution of the vibrational spectrum reveals the ultrafast structural changes that occur during the charge separation (Franck-Condon excited state complex → contact ion pair) and the subsequent charge recombination (contact ion pair → ground state complex). The Franck-Condon excited state is shown to have significant charge-separated character because its vibrational spectrum is similar to that of the ion pair. The charge separation rate (2.5 ps in ethylacetate and ∼0.5 ps in acetonitrile) is comparable to solvation dynamics and is unaffected by the perdeuteration of HMB, supporting the dominant role of solvent rearrangement in charge separation. On the other hand, the charge recombination slows by a factor of ∼1.4 when using perdeuterated HMB, indicating that methyl hydrogen motions of HMB mediate the charge recombination process. Resonance Raman enhancement of the HMB vibrations in the complex reveals that the ring stretches of HMB, and especially the C-CH(3) deformations are the primary acceptor modes promoting charge recombination.

Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.

Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, themore » 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.« less

Photon echo spectroscopy reveals structure-dynamics relationships in carotenoids

NASA Astrophysics Data System (ADS)

Christensson, N.; Polivka, T.; Yartsev, A.; Pullerits, T.

2009-06-01

Based on simultaneous analysis of the frequency-resolved transient grating, peak shift, and echo width signals, we present a model for the third-order optical response of carotenoids including population dynamics and system-bath interactions. Our frequency-resolved photon echo experiments show that the model needs to incorporate the excited-state absorption from both the S2 and the S1 states. We apply our model to analyze the experimental results on astaxanthin and lycopene, aiming to elucidate the relation between structure and system-bath interactions. Our analysis allows us to relate structural motifs to changes in the energy-gap correlation functions. We find that the terminal rings of astaxanthin lead to increased coupling between slow molecular motions and the electronic transition. We also find evidence for stronger coupling to higher frequency overdamped modes in astaxanthin, pointing to the importance of the functional groups in providing coupling to fluctuations influencing the dynamics in the passage through the conical intersection governing the S2-S1 relaxation.

Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: A molecular dynamics study.

PubMed

Wang, Lingyun; Yan, Feng

2017-10-01

Protein phosphatase 5 (PP5), mainly localized in human brain, can dephosphorylate tau protein whose high level of phosphorylation is related to Alzheimer's disease. Similar to other protein phosphatases, PP5 has a conserved motif in the catalytic domain that contains two binding sites for manganese (Mn 2+ ) ions. Structural data indicate that two active site water molecules, one bridging the two Mn 2+ ions and the other terminally coordinated with one of the Mn 2+ ions (Mn1), are involved in catalysis. Recently, a density functional theory study revealed that the two water molecules can be both deprotonated to keep a neutral active site for catalysis. The theoretical study gives us an insight into the catalytic mechanism of PP5, but the knowledge of how the deprotonation states of the two water molecules affect the binding of PP5 with its substrate is still lacking. To approach this problem, molecular dynamics simulations were performed to model the four possible deprotonation states. Through structural, dynamical and energetic analyses, the results demonstrate that the deprotonation states of the two water molecules affect the structure of the active site including the distance between the two Mn 2+ ions and their coordination, impact the interaction energy of residues R275, R400 and H304 which directly interact with the substrate phosphoserine, and mediate the dynamics of helix αJ which is involved in regulation of the enzyme's activity. Furthermore, the deprotonation state that is preferable for PP5 binding of its substrate has been identified. These findings could provide new design strategy for PP5 inhibitor. © 2017 The Protein Society.

Conference Proceedings of NASA/DoD Controls-Structures Interaction Technology Held in San Diego, California on 29 January-2 February 1989,

DTIC Science & Technology

1989-08-01

NASA Langley Research Center, Hampton, Virginia, and Wright Research Development Center, Wright-Patterson Air Force Base, Ohio, and held in San Diego...427 Shalom Fisher SPACE TRUSS ZERO GRAVITY DYNAMICS. ............................... 445 Captain Andy Swanson UNITED STATES AIR FORCE ACADEMY GET-AWAY...HOUSE EXPERIMENTS IN LARGE SPACE STRUCTURES AT THE AIR FORCE WRIGHT AERONAUTICAL LABORATORIES FLIGHT DYNAMICS LABORATORY

Force-Manipulation Single-Molecule Spectroscopy Studies of Enzymatic Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter; He, Yufan; Lu, Maolin; Cao, Jin; Guo, Qing

2014-03-01

Subtle conformational changes play a crucial role in protein functions, especially in enzymatic reactions involving complex substrate-enzyme interactions and chemical reactions. We applied AFM-enhanced and magnetic tweezers-correlated single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing. Our results support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation

PubMed Central

Toraya, Shuichi; Javkhlantugs, Namsrai; Mishima, Daisuke; Nishimura, Katsuyuki; Ueda, Kazuyoshi; Naito, Akira

2010-01-01

Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state 31P and 13C NMR spectroscopy. 31P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (Tc) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the Tc. 13C NMR spectra of site-specifically 13C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers. PMID:21081076

Active influence in dynamical models of structural balance in social networks

NASA Astrophysics Data System (ADS)

Summers, Tyler H.; Shames, Iman

2013-07-01

We consider a nonlinear dynamical system on a signed graph, which can be interpreted as a mathematical model of social networks in which the links can have both positive and negative connotations. In accordance with a concept from social psychology called structural balance, the negative links play a key role in both the structure and dynamics of the network. Recent research has shown that in a nonlinear dynamical system modeling the time evolution of “friendliness levels” in the network, two opposing factions emerge from almost any initial condition. Here we study active external influence in this dynamical model and show that any agent in the network can achieve any desired structurally balanced state from any initial condition by perturbing its own local friendliness levels. Based on this result, we also introduce a new network centrality measure for signed networks. The results are illustrated in an international-relations network using United Nations voting record data from 1946 to 2008 to estimate friendliness levels amongst various countries.

The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks.

PubMed

Landau, Itamar D; Egger, Robert; Dercksen, Vincent J; Oberlaender, Marcel; Sompolinsky, Haim

2016-12-07

Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Complementary study of molecular dynamics and domain sizes in heterogenous nanocomposites PBT/DA-C{sub 60} and PBT/TCNEO-C{sub 60}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woźniak-Braszak, A., E-mail: abraszak@amu.edu.pl; Baranowski, M.; Jurga, K.

2014-05-28

A comprehensive study of molecular dynamics and structure in new heterogenous nanocomposites based on poly(butylene terephthalate) and nanoparticles C{sub 60} modified by n-decylamine or tetracyanoethylene oxide has been performed. The domain structure of new nanocomposites has been investigated by Fourier transform infrared spectroscopy, wide-angle X-ray scattering, and differential scanning calorimetry techniques. Solid-state {sup 1}H NMR techniques were used to study molecular dynamics and domain sizes in new nanocomposites. Information about the electronic properties of these nanocomposites was obtained by means of electron paramagnetic resonance method. It was shown that the structure and molecular dynamics of new nanocomposites were strongly dependentmore » on the properties and concentration of fullerene derivates.« less

X-56A MUTT: Aeroservoelastic Modeling

NASA Technical Reports Server (NTRS)

Ouellette, Jeffrey A.

2015-01-01

For the NASA X-56a Program, Armstrong Flight Research Center has been developing a set of linear states space models that integrate the flight dynamics and structural dynamics. These high order models are needed for the control design, control evaluation, and test input design. The current focus has been on developing stiff wing models to validate the current modeling approach. The extension of the modeling approach to the flexible wings requires only a change in the structural model. Individual subsystems models (actuators, inertial properties, etc.) have been validated by component level ground tests. Closed loop simulation of maneuvers designed to validate the flight dynamics of these models correlates very well flight test data. The open loop structural dynamics are also shown to correlate well to the flight test data.

An ab initio study of the structure and dynamics of bulk liquid Cd and its liquid-vapor interface.

PubMed

Calderín, L; González, L E; González, D J

2013-02-13

Several static and dynamic properties of bulk liquid Cd at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported for several transport coefficients. Additional simulations have also been performed at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behavior with two different wavelengths, as the spacing between the outer and first inner layer is different from that between the other inner layers. The calculated reflectivity shows a marked maximum whose origin is related to the surface layering, along with a shoulder located at a much smaller wavevector transfer.

Charge Separation and Exciton Dynamics at Polymer/ZnO Interface from First-Principles Simulations.

PubMed

Wu, Guangfen; Li, Zi; Zhang, Xu; Lu, Gang

2014-08-07

Charge separation and exciton dynamics play a crucial role in determining the performance of excitonic photovoltaics. Using time-dependent density functional theory with a range-separated exchange-correlation functional as well as nonadiabatic ab initio molecular dynamics, we have studied the formation and dynamics of charge-transfer (CT) excitons at polymer/ZnO interface. The interfacial atomic structure, exciton density of states and conversions between exciton species are examined from first-principles. The exciton dynamics exhibits both adiabatic and nonadiabatic characters. While the adiabatic transitions are facilitated by C═C vibrations along the polymer (P3HT) backbone, the nonadiabatic transitions are realized by exciton hopping between the excited states. We find that the localized ZnO surface states lead to localized low-energy CT states and poor charge separation. In contrast, the surface states of crystalline C60 are indistinguishable from the bulk states, resulting in delocalized CT states and efficient charge separation in polymer/fullerene (P3HT/PCBM) heterojunctions. The hot CT states are found to cool down in an ultrafast time scale and may not play a major role in charge separation of P3HT/ZnO. Finally we suggest that the dimensions of nanostructured acceptors can be tuned to obtain both efficient charge separation and high open circuit voltages.

Theoretical study of dynamic electron-spin-polarization via the doublet-quartet quantum-mixed state and time-resolved ESR spectra of the quartet high-spin state.

PubMed

Teki, Yoshio; Matsumoto, Takafumi

2011-04-07

The mechanism of the unique dynamic electron polarization of the quartet (S = 3/2) high-spin state via a doublet-quartet quantum-mixed state and detail theoretical calculations of the population transfer are reported. By the photo-induced electron transfer, the quantum-mixed charge-separate state is generated in acceptor-donor-radical triad (A-D-R). This mechanism explains well the unique dynamic electron polarization of the quartet state of A-D-R. The generation of the selectively populated quantum-mixed state and its transfer to the strongly coupled pure quartet and doublet states have been treated both by a perturbation approach and by exact numerical calculations. The analytical solutions show that generation of the quantum-mixed states with the selective populations after de-coherence and/or accompanying the (complete) dephasing during the charge-recombination are essential for the unique dynamic electron polarization. Thus, the elimination of the quantum coherence (loss of the quantum information) is the key process for the population transfer from the quantum-mixed state to the quartet state. The generation of high-field polarization on the strongly coupled quartet state by the charge-recombination process can be explained by a polarization transfer from the quantum-mixed charge-separate state. Typical time-resolved ESR patterns of the quantum-mixed state and of the strongly coupled quartet state are simulated based on the generation mechanism of the dynamic electron polarization. The dependence of the spectral pattern of the quartet high-spin state has been clarified for the fine-structure tensor and the exchange interaction of the quantum-mixed state. The spectral pattern of the quartet state is not sensitive towards the fine-structure tensor of the quantum-mixed state, because this tensor contributes only as a perturbation in the population transfer to the spin-sublevels of the quartet state. Based on the stochastic Liouville equation, it is also discussed why the selective population in the quantum-mixed state is generated for the "finite field" spin-sublevels. The numerical calculations of the elimination of the quantum coherence (de-coherence and/or dephasing) are demonstrated. A new possibility of the enhanced intersystem crossing pathway in solution is also proposed.

Dramatic effect of single-base mutation on the conformational dynamics of human telomeric G-quadruplex

PubMed Central

Lee, Ja Yil; Kim, D. S.

2009-01-01

Guanine-rich DNA sequences can form G-quadruplexes. These four-stranded structures are known to form in several genomic regions and to influence certain biological activities. Sometimes, the instability of G-quadruplexes causes the abnormal biological processes. Mutation is a culprit for the destabilization of G-quadruplexes, but the details of mutated G-quadruplexes are poorly understood. In this article, we investigated the conformational dynamics of single-base mutated human telomeric G-quadruplexes in the presence of K+ with single-molecule FRET spectroscopy. We observed that the replacement of single guanine by thymine in a G-track induces various folded structures, i.e. structural polymorphism. Moreover, direct observation of their dynamics revealed that a single-base mutation causes fast unfolding of folded states under physiological conditions. Furthermore, we found that the degree of destabilization varies according to mutation positions. When the central guanine of a G-track is replaced, the G-quadruplexes unfold quickly at any K+ concentrations and temperature. Meanwhile, outer-quartet mutated G-quadruplexes have heterogeneous dynamics at intermediate K+ concentrations and longstanding folded states at high K+ concentrations. Several factors such as base-stacking interaction and K+ coordination are responsible for the different dynamics according to the mutation position. PMID:19359361

Different evolution dynamics of vector solitons depending on their polarization states

NASA Astrophysics Data System (ADS)

Chen, Wei-Cheng; Chen, Guo-Jie

2014-03-01

There are three types of temporal evolution dynamics of vector solitons observed in a ring fiber laser with a semiconductor saturable absorption mirror (SESAM) as a mode-locker. It is found that the polarization property of vector solitons is an important factor for achieving different evolution dynamics. The vector soliton with a uniform polarization state across the whole pulse profile and zero polarization extinction ratio operates at a fundamental repetition rate with a single pulse profile. The elliptically polarized vector soliton with a larger polarization extinction ratio exhibits a harmonic pulse train. The soliton bunching with multi-peak structures exists between the above two states and shows elliptical polarization with a small polarization extinction ratio.

Modeling the Car Crash Crisis Management System Using HiLA

NASA Astrophysics Data System (ADS)

Hölzl, Matthias; Knapp, Alexander; Zhang, Gefei

An aspect-oriented modeling approach to the Car Crash Crisis Management System (CCCMS) using the High-Level Aspect (HiLA) language is described. HiLA is a language for expressing aspects for UML static structures and UML state machines. In particular, HiLA supports both a static graph transformational and a dynamic approach of applying aspects. Furthermore, it facilitates methodologically turning use case descriptions into state machines: for each main success scenario, a base state machine is developed; all extensions to this main success scenario are covered by aspects. Overall, the static structure of the CCCMS is modeled in 43 classes, the main success scenarios in 13 base machines, the use case extensions in 47 static and 31 dynamic aspects, most of which are instantiations of simple aspect templates.

Ultrafast 25-fs relaxation in highly excited states of methyl azide mediated by strong nonadiabatic coupling.

PubMed

Peters, William K; Couch, David E; Mignolet, Benoit; Shi, Xuetao; Nguyen, Quynh L; Fortenberry, Ryan C; Schlegel, H Bernhard; Remacle, Françoise; Kapteyn, Henry C; Murnane, Margaret M; Li, Wen

2017-12-26

Highly excited electronic states are challenging to explore experimentally and theoretically-due to the large density of states and the fact that small structural changes lead to large changes in electronic character with associated strong nonadiabatic dynamics. They can play a key role in astrophysical and ionospheric chemistry, as well as the detonation chemistry of high-energy density materials. Here, we implement ultrafast vacuum-UV (VUV)-driven electron-ion coincidence imaging spectroscopy to directly probe the reaction pathways of highly excited states of energetic molecules-in this case, methyl azide. Our data, combined with advanced theoretical simulations, show that photoexcitation of methyl azide by a 10-fs UV pulse at 8 eV drives fast structural changes and strong nonadiabatic coupling that leads to relaxation to other excited states on a surprisingly fast timescale of 25 fs. This ultrafast relaxation differs from dynamics occurring on lower excited states, where the timescale required for the wavepacket to reach a region of strong nonadiabatic coupling is typically much longer. Moreover, our theoretical calculations show that ultrafast relaxation of the wavepacket to a lower excited state occurs along one of the conical intersection seams before reaching the minimum energy conical intersection. These findings are important for understanding the unique strongly coupled non-Born-Oppenheimer molecular dynamics of VUV-excited energetic molecules. Although such observations have been predicted for many years, this study represents one of the few where such strongly coupled non-Born-Oppenheimer molecular dynamics of VUV-excited energetic molecules have been conclusively observed directly, making it possible to identify the ultrafast reaction pathways.

Dynamic fiber Bragg gratings based health monitoring system of composite aerospace structures

NASA Astrophysics Data System (ADS)

Panopoulou, A.; Loutas, T.; Roulias, D.; Fransen, S.; Kostopoulos, V.

2011-09-01

The main purpose of the current work is to develop a new system for structural health monitoring of composite aerospace structures based on real-time dynamic measurements, in order to identify the structural state condition. Long-gauge Fibre Bragg Grating (FBG) optical sensors were used for monitoring the dynamic response of the composite structure. The algorithm that was developed for structural damage detection utilizes the collected dynamic response data, analyzes them in various ways and through an artificial neural network identifies the damage state and its location. Damage was simulated by slightly varying locally the mass of the structure (by adding a known mass) at different zones of the structure. Lumped masses in different locations upon the structure alter the eigen-frequencies in a way similar to actual damage. The structural dynamic behaviour has been numerically simulated and experimentally verified by means of modal testing on two different composite aerospace structures. Advanced digital signal processing techniques, e.g. the wavelet transform (WT), were used for the analysis of the dynamic response for feature extraction. WT's capability of separating the different frequency components in the time domain without loosing frequency information makes it a versatile tool for demanding signal processing applications. The use of WT is also suggested by the no-stationary nature of dynamic response signals and the opportunity of evaluating the temporal evolution of their frequency contents. Feature extraction is the first step of the procedure. The extracted features are effective indices of damage size and location. The classification step comprises of a feed-forward back propagation network, whose output determines the simulated damage location. Finally, dedicated training and validation activities were carried out by means of numerical simulations and experimental procedures. Experimental validation was performed initially on a flat stiffened panel, representing a section of a typical aeronautical structure, manufactured and tested in the lab and, as a second step, on a scaled up space oriented structure, which is a composite honeycomb plate, used as a deployment base for antenna arrays. An integrated FBG sensor network, based on the advantage of multiplexing, was mounted on both structures and different excitation positions and boundary conditions were used. The analysis of operational dynamic responses was employed to identify both the damage and its position. The system that was designed and tested initially on the thin composite panel, was successfully validated on the larger honeycomb structure. Numerical simulation of both structures was used as a support tool at all the steps of the work providing among others the location of the optical sensors used. The proposed work will be the base for the whole system qualification and validation on an antenna reflector in future work.

Real time observation of the excimer formation dynamics of a gas phase benzene dimer by picosecond pump-probe spectroscopy.

PubMed

Miyazaki, Mitsuhiko; Fujii, Masaaki

2015-10-21

We observed the real-time excimer (EXC) formation dynamics of a gas phase benzene dimer (Bz2) cluster after photo-excitation to the S1 state by applying an ionization detected picosecond transient absorption method for probing the visible EXC absorption for the first time. The time evolution of the EXC absorption from the S1 0(0) level shows a rise that is well fitted by a single exponential function with a time constant of 18 ± 2 ps. The structure of the Bz dimer has a T-shaped structure in the ground electronic state, and that in the EXC state is a parallel sandwich (SW) structure. Thus, the observed rise time corresponds to the structural change from the T to the SW structures, which directly shows the EXC formation. On the other hand, the EXC formation after excitation of the S1 6(1) vibrational level of the stem site showed a faster rise of the time constant of 10 ± 2 ps. Supposing equilibrium between the EXC and the local excited states, it followed that the intramolecular vibrational energy redistribution rate of the 6(1) level is largely enhanced and becomes faster than the EXC formation reaction.

Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser.

PubMed

Beyerlein, Kenneth R; Jönsson, H Olof; Alonso-Mori, Roberto; Aquila, Andrew; Bajt, Saša; Barty, Anton; Bean, Richard; Koglin, Jason E; Messerschmidt, Marc; Ragazzon, Davide; Sokaras, Dimosthenis; Williams, Garth J; Hau-Riege, Stefan; Boutet, Sébastien; Chapman, Henry N; Tîmneanu, Nicuşor; Caleman, Carl

2018-05-29

The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 10 6 J/cm 2 These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules

PubMed Central

Schanda, Paul; Ernst, Matthias

2016-01-01

Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution. PMID:27110043

Visualizing the dynamic structure of the plant photosynthetic membrane.

PubMed

Ruban, Alexander V; Johnson, Matthew P

2015-11-03

The chloroplast thylakoid membrane is the site for the initial steps of photosynthesis that convert solar energy into chemical energy, ultimately powering almost all life on earth. The heterogeneous distribution of protein complexes within the membrane gives rise to an intricate three-dimensional structure that is nonetheless extremely dynamic on a timescale of seconds to minutes. These dynamics form the basis for the regulation of photosynthesis, and therefore the adaptability of plants to different environments. High-resolution microscopy has in recent years begun to provide new insights into the structural dynamics underlying a number of regulatory processes such as membrane stacking, photosystem II repair, photoprotective energy dissipation, state transitions and alternative electron transfer. Here we provide an overview of the essentials of thylakoid membrane structure in plants, and consider how recent advances, using a range of microscopies, have substantially increased our knowledge of the thylakoid dynamic structure. We discuss both the successes and limitations of the currently available techniques and highlight newly emerging microscopic methods that promise to move the field beyond the current 'static' view of membrane organization based on frozen snapshots to a 'live' view of functional membranes imaged under native aqueous conditions at ambient temperature and responding dynamically to external stimuli.

On the influence of dynamic stress variations on strain accumulation in fault zones

NASA Astrophysics Data System (ADS)

Grigoriev, A. S.; Shilko, E. V.; Astafurov, S. V.; Dimaki, A. V.; Vysotsky, E. M.; Psakhie, S. G.

2015-10-01

In this paper, a numerical study of the influence of the stress state of interface of the block medium structural elements on the deformation response of interface to the dynamic impacts. It is shown that the basic characteristics of the stress state determining the deformation response of the interface are the values of shear stress and mean stress. It is found that the dependence of the irreversible displacement at the interface zone initiated by dynamic impact on the reduced shear stress is described by the logistic function. Herewith, the influence of the mean stress and dynamic impact energy on the value of displacement initiated by dynamic impact can be taken into account by dependence of the logistic function numerator on these parameters.

Bifurcation structure of localized states in the Lugiato-Lefever equation with anomalous dispersion

NASA Astrophysics Data System (ADS)

Parra-Rivas, P.; Gomila, D.; Gelens, L.; Knobloch, E.

2018-04-01

The origin, stability, and bifurcation structure of different types of bright localized structures described by the Lugiato-Lefever equation are studied. This mean field model describes the nonlinear dynamics of light circulating in fiber cavities and microresonators. In the case of anomalous group velocity dispersion and low values of the intracavity phase detuning these bright states are organized in a homoclinic snaking bifurcation structure. We describe how this bifurcation structure is destroyed when the detuning is increased across a critical value, and determine how a bifurcation structure known as foliated snaking emerges.

Discrete Kalman filtering equations of second-order form for control-structure interaction simulations

NASA Technical Reports Server (NTRS)

Park, K. C.; Alvin, K. F.; Belvin, W. Keith

1991-01-01

A second-order form of discrete Kalman filtering equations is proposed as a candidate state estimator for efficient simulations of control-structure interactions in coupled physical coordinate configurations as opposed to decoupled modal coordinates. The resulting matrix equation of the present state estimator consists of the same symmetric, sparse N x N coupled matrices of the governing structural dynamics equations as opposed to unsymmetric 2N x 2N state space-based estimators. Thus, in addition to substantial computational efficiency improvement, the present estimator can be applied to control-structure design optimization for which the physical coordinates associated with the mass, damping and stiffness matrices of the structure are needed instead of modal coordinates.

Ultrafast excited-state dynamics of RNA and DNA C tracts

NASA Astrophysics Data System (ADS)

Cohen, Boiko; Larson, Matthew H.; Kohler, Bern

2008-06-01

The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC) 18 were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC) 18 at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ˜100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.

Research on FBG-Based CFRP Structural Damage Identification Using BP Neural Network

NASA Astrophysics Data System (ADS)

Geng, Xiangyi; Lu, Shizeng; Jiang, Mingshun; Sui, Qingmei; Lv, Shanshan; Xiao, Hang; Jia, Yuxi; Jia, Lei

2018-06-01

A damage identification system of carbon fiber reinforced plastics (CFRP) structures is investigated using fiber Bragg grating (FBG) sensors and back propagation (BP) neural network. FBG sensors are applied to construct the sensing network to detect the structural dynamic response signals generated by active actuation. The damage identification model is built based on the BP neural network. The dynamic signal characteristics extracted by the Fourier transform are the inputs, and the damage states are the outputs of the model. Besides, damages are simulated by placing lumped masses with different weights instead of inducing real damages, which is confirmed to be feasible by finite element analysis (FEA). At last, the damage identification system is verified on a CFRP plate with 300 mm × 300 mm experimental area, with the accurate identification of varied damage states. The system provides a practical way for CFRP structural damage identification.

Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V., E-mail: sergeid@kth.se

2016-01-21

Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental datamore » obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees.« less

Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation.

PubMed

Sharma, Anirban; Ghorai, Pradip Kr

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

Effect of water on structure and dynamics of [BMIM][PF{sub 6}] ionic liquid: An all-atom molecular dynamics simulation investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Anirban; Ghorai, Pradip Kr., E-mail: pradip@iiserkol.ac.in

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF{sub 6}]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure ILmore » but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.« less

Relating dynamics of model unentangled, crystallizable polymeric liquids to their local structure

NASA Astrophysics Data System (ADS)

Nguyen, Hong T.; Hoy, Robert S.

We study the liquid-state dynamics of a recently developed, crystallizable bead-spring polymer model. The model possesses a single ground state (NCP, wherein monomers close-pack and chains are nematically aligned) for all finite bending stiffnesses kb, but the solid morphologies formed under cooling vary strongly with kb, varying from NCP to amorphous. We find that systems with kb producing amorphous order are good glass-formers exhibiting the classic Vogel-Fulcher slowdown with decreasing temperature T. In contrast, systems with kb producing crystalline solids exhibit a simpler dynamics when kb is small. Larger kb produce more complex dynamics, but these are associated with the existence of an intermediate nematic liquid rather than glassy slowdown. We relate these differences to local, cluster-level structure measured via TCC analyses. Formation propensities and lifetimes of various clusters (associated with amorphous or crystalline order) vary strongly with kb and T. We relate these differences to those measured by the self-intermediate scattering function and other macroscopic measures of dynamics. Our results should aid in understanding the competition between crystallization and glass-formation in synthetic polymers.

Taking the plunge: chemical reaction dynamics in liquids.

PubMed

Orr-Ewing, Andrew J

2017-12-11

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

Static, dynamic and electronic properties of expanded fluid mercury in the metal-nonmetal transition range. An ab initio study.

PubMed

Calderín, L; González, L E; González, D J

2011-09-21

Fluid Hg undergoes a metal-nonmetal (M-NM) transition when expanded toward a density of around 9 g cm(-3). We have performed ab initio molecular dynamics simulations for several thermodynamic states around the M-NM transition range and the associated static, dynamic and electronic properties have been analyzed. The calculated static structure shows a good agreement with the available experimental data. It is found that the volume expansion decreases the number of nearest neighbors from 10 (near the triple point) to around 8 at the M-NM transition region. Moreover, these neighbors are arranged into two subshells and the decrease in the number of neighbors occurs in the inner subshell. The calculated dynamic structure factors agree fairly well with their experimental counterparts obtained by inelastic x-ray scattering experiments, which display inelastic side peaks. The derived dispersion relation exhibits some positive dispersion for all the states, although its value around the M-NM transition region is not as marked as suggested by the experiment. We have also calculated the electronic density of states, which shows the appearance of a gap at a density of around 8.3 g cm(-3).

Investigation of Local Structures in Cation-ordered Microwave Dielectric A Solid-state NMR and First Principle Calculation Study

NASA Astrophysics Data System (ADS)

Kalfarisi, Rony G.

Solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy has proven to be a powerful method to probe the local structure and dynamics of a system. In powdered solids, the nuclear spins experience various anisotropic interactions which depend on the molecular orientation. These anisotropic interactions make ssNMR very useful as they give a specific appearance to the resonance lines of the spectra. The position and shape of these resonance lines can be related to local structure and dynamics of the system under study. My research interest has focused around studying local structures and dynamics of quadrupolar nuclei in materials using ssNMR spectroscopy. 7Li and 93Nb ssNMR magic angle spinning (MAS) spectra, acquired at 17.6 and 7.06 T, have been used to evaluate the structural and dynamical properties of cation-ordered microwave dielectric materials. Microwave dielectric materials are essential in the application of wireless telecommunication, biomedical engineering, and other scientific and industrial implementations that use radio and microwave signals. The study of the local environment with respect to average structure, such as X-ray diffraction study, is essential for the better understanding of the correlations between structures and properties of these materials. The investigation for short and medium range can be performed with the use of ssNMR techniques. Even though XRD results show cationic ordering at the B-site (third coordination sphere), NMR spectra show a presence of disorder materials. This was indicated by the observation of a distribution in NMR parameters derived from experimental . {93}Nb NMR spectraand supported by theoretical calculations.

Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations

PubMed Central

2015-01-01

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4–ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level. PMID:25231537

Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2014-10-14

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4-ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level.

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

DOE PAGES

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus; ...

2018-02-20

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I

NASA Astrophysics Data System (ADS)

Venditti, Vincenzo; Tugarinov, Vitali; Schwieters, Charles D.; Grishaev, Alexander; Clore, G. Marius

2015-01-01

Enzyme I (EI), the first component of the bacterial phosphotransfer signal transduction system, undergoes one of the largest substrate-induced interdomain rearrangements documented to date. Here we characterize the perturbations generated by two small molecules, the natural substrate phosphoenolpyruvate and the inhibitor α-ketoglutarate, on the structure and dynamics of EI using NMR, small-angle X-ray scattering and biochemical techniques. The results indicate unambiguously that the open-to-closed conformational switch of EI is triggered by complete suppression of micro- to millisecond dynamics within the C-terminal domain of EI. Indeed, we show that a ligand-induced transition from a dynamic to a more rigid conformational state of the C-terminal domain stabilizes the interface between the N- and C-terminal domains observed in the structure of the closed state, thereby promoting the resulting conformational switch and autophosphorylation of EI. The mechanisms described here may be common to several other multidomain proteins and allosteric systems.

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy

PubMed Central

Khambhati, Ankit N.; Davis, Kathryn A.; Oommen, Brian S.; Chen, Stephanie H.; Lucas, Timothy H.; Litt, Brian; Bassett, Danielle S.

2015-01-01

The epileptic network is characterized by pathologic, seizure-generating ‘foci’ embedded in a web of structural and functional connections. Clinically, seizure foci are considered optimal targets for surgery. However, poor surgical outcome suggests a complex relationship between foci and the surrounding network that drives seizure dynamics. We developed a novel technique to objectively track seizure states from dynamic functional networks constructed from intracranial recordings. Each dynamical state captures unique patterns of network connections that indicate synchronized and desynchronized hubs of neural populations. Our approach suggests that seizures are generated when synchronous relationships near foci work in tandem with rapidly changing desynchronous relationships from the surrounding epileptic network. As seizures progress, topographical and geometrical changes in network connectivity strengthen and tighten synchronous connectivity near foci—a mechanism that may aid seizure termination. Collectively, our observations implicate distributed cortical structures in seizure generation, propagation and termination, and may have practical significance in determining which circuits to modulate with implantable devices. PMID:26680762

Control Augmented Structural Synthesis

NASA Technical Reports Server (NTRS)

Lust, Robert V.; Schmit, Lucien A.

1988-01-01

A methodology for control augmented structural synthesis is proposed for a class of structures which can be modeled as an assemblage of frame and/or truss elements. It is assumed that both the plant (structure) and the active control system dynamics can be adequately represented with a linear model. The structural sizing variables, active control system feedback gains and nonstructural lumped masses are treated simultaneously as independent design variables. Design constraints are imposed on static and dynamic displacements, static stresses, actuator forces and natural frequencies to ensure acceptable system behavior. Multiple static and dynamic loading conditions are considered. Side constraints imposed on the design variables protect against the generation of unrealizable designs. While the proposed approach is fundamentally more general, here the methodology is developed and demonstrated for the case where: (1) the dynamic loading is harmonic and thus the steady state response is of primary interest; (2) direct output feedback is used for the control system model; and (3) the actuators and sensors are collocated.

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

Peptoid nanosheets exhibit a new secondary-structure motif.

PubMed

Mannige, Ranjan V; Haxton, Thomas K; Proulx, Caroline; Robertson, Ellen J; Battigelli, Alessia; Butterfoss, Glenn L; Zuckermann, Ronald N; Whitelam, Stephen

2015-10-15

A promising route to the synthesis of protein-mimetic materials that are capable of complex functions, such as molecular recognition and catalysis, is provided by sequence-defined peptoid polymers--structural relatives of biologically occurring polypeptides. Peptoids, which are relatively non-toxic and resistant to degradation, can fold into defined structures through a combination of sequence-dependent interactions. However, the range of possible structures that are accessible to peptoids and other biological mimetics is unknown, and our ability to design protein-like architectures from these polymer classes is limited. Here we use molecular-dynamics simulations, together with scattering and microscopy data, to determine the atomic-resolution structure of the recently discovered peptoid nanosheet, an ordered supramolecular assembly that extends macroscopically in only two dimensions. Our simulations show that nanosheets are structurally and dynamically heterogeneous, can be formed only from peptoids of certain lengths, and are potentially porous to water and ions. Moreover, their formation is enabled by the peptoids' adoption of a secondary structure that is not seen in the natural world. This structure, a zigzag pattern that we call a Σ('sigma')-strand, results from the ability of adjacent backbone monomers to adopt opposed rotational states, thereby allowing the backbone to remain linear and untwisted. Linear backbones tiled in a brick-like way form an extended two-dimensional nanostructure, the Σ-sheet. The binary rotational-state motif of the Σ-strand is not seen in regular protein structures, which are usually built from one type of rotational state. We also show that the concept of building regular structures from multiple rotational states can be generalized beyond the peptoid nanosheet system.

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proven to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

PubMed

Lewis, Nicholas H C; Dong, Hui; Oliver, Thomas A A; Fleming, Graham R

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

PubMed Central

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M.; Menzel, Andreas; Fersht, Alan R.; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution. PMID:25946337

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

PubMed

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L; Freund, Stefan M; Menzel, Andreas; Fersht, Alan R; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Circular dichroism and site-directed spin labeling reveal structural and dynamical features of high-pressure states of myoglobin

PubMed Central

Lerch, Michael T.; Horwitz, Joseph; McCoy, John; Hubbell, Wayne L.

2013-01-01

Excited states of proteins may play important roles in function, yet are difficult to study spectroscopically because of their sparse population. High hydrostatic pressure increases the equilibrium population of excited states, enabling their characterization [Akasaka K (2003) Biochemistry 42:10875–85]. High-pressure site-directed spin-labeling EPR (SDSL-EPR) was developed recently to map the site-specific structure and dynamics of excited states populated by pressure. To monitor global secondary structure content by circular dichroism (CD) at high pressure, a modified optical cell using a custom MgF2 window with a reduced aperture is introduced. Here, a combination of SDSL-EPR and CD is used to map reversible structural transitions in holomyoglobin and apomyoglobin (apoMb) as a function of applied pressure up to 2 kbar. CD shows that the high-pressure excited state of apoMb at pH 6 has helical content identical to that of native apoMb, but reversible changes reflecting the appearance of a conformational ensemble are observed by SDSL-EPR, suggesting a helical topology that fluctuates slowly on the EPR time scale. Although the high-pressure state of apoMb at pH 6 has been referred to as a molten globule, the data presented here reveal significant differences from the well-characterized pH 4.1 molten globule of apoMb. Pressure-populated states of both holomyoglobin and apoMb at pH 4.1 have significantly less helical structure, and for the latter, that may correspond to a transient folding intermediate. PMID:24248390

Nonadiabatic dynamics simulation of photoisomerization mechanism of the second stablest isomer of N-salicilydenemethylfurylamine

NASA Astrophysics Data System (ADS)

Gao, Aihua; Li, Jianpeng; Wang, Dehua; Ma, Xiaoguang; Wang, Meishan

2018-02-01

The photoisomerization processes of the second stablest isomer in the aromatic Schiff base, N-salicilydenemethylfurylamine, in the gas phase have been studied by static electronic structure calculations and surface-hopping dynamics simulations based on the Zhu-Nakamura theory. Various stable structures are obtained in the optimization because of different orientations of methyl-furyl part with respect to the salicylaldimine part and different orientations of hydroxy group with respect to the benzene ring. Upon photoexcitation into the first excited state, bond isomerization in the salicylaldimine part is completely suppressed until the strong excited-state hydrogen bond is broken. The decay pathway involves two excited-state minima, one in cis-enol form and the other in cis-keto form. After the excited-state proton transfer, twists of bonds lead to a conical intersection between the ground and excited states. After internal conversion around a conical intersection, the molecule is stabilized in cis- or trans-keto form. If the reverse hydrogen transfer process occurs in the ground state, the molecule will finally end up in the cis-enol region. The cis-keto and trans-keto isomers are observed as photoproducts. According to our full-dimensional nonadiabatic dynamics simulations, we find the excited-state intramolecular proton transfer and torsions of three single bonds in the chain to be responsible for photoisomerization of the second stablest isomer of N-salicilydenemethylfurylamine.

Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent.

PubMed

Zhang, Yuyuan; de La Harpe, Kimberly; Hariharan, Mahesh; Kohler, Bern

2018-04-17

The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation

PubMed Central

Sereda, Yuriy V.; Singharoy, Abhishek B.; Jarrold, Martin F.; Ortoleva, Peter J.

2012-01-01

An approach for the automated discovery of low free energy states of macromolecular systems is presented. The method does not involve delineating the entire free energy landscape but proceeds in a sequential free energy minimizing state discovery, i.e., it first discovers one low free energy state and then automatically seeks a distinct neighboring one. These states and the associated ensembles of atomistic configurations are characterized by coarse-grained variables capturing the large-scale structure of the system. A key facet of our approach is the identification of such coarse-grained variables. Evolution of these variables is governed by Langevin dynamics driven by thermal-average forces and mediated by diffusivities, both of which are constructed by an ensemble of short molecular dynamics runs. In the present approach, the thermal-average forces are modified to account for the entropy changes following from our knowledge of the free energy basins already discovered. Such forces guide the system away from the known free energy minima, over free energy barriers, and to a new one. The theory is demonstrated for lactoferrin, known to have multiple energy-minimizing structures. The approach is validated using experimental structures and traditional molecular dynamics. The method can be generalized to enable the interpretation of nanocharacterization data (e.g., ion mobility – mass spectrometry, atomic force microscopy, chemical labeling, and nanopore measurements). PMID:22423635

Persistent Topology and Metastable State in Conformational Dynamics

PubMed Central

Chang, Huang-Wei; Bacallado, Sergio; Pande, Vijay S.; Carlsson, Gunnar E.

2013-01-01

The large amount of molecular dynamics simulation data produced by modern computational models brings big opportunities and challenges to researchers. Clustering algorithms play an important role in understanding biomolecular kinetics from the simulation data, especially under the Markov state model framework. However, the ruggedness of the free energy landscape in a biomolecular system makes common clustering algorithms very sensitive to perturbations of the data. Here, we introduce a data-exploratory tool which provides an overview of the clustering structure under different parameters. The proposed Multi-Persistent Clustering analysis combines insights from recent studies on the dynamics of systems with dominant metastable states with the concept of multi-dimensional persistence in computational topology. We propose to explore the clustering structure of the data based on its persistence on scale and density. The analysis provides a systematic way to discover clusters that are robust to perturbations of the data. The dominant states of the system can be chosen with confidence. For the clusters on the borderline, the user can choose to do more simulation or make a decision based on their structural characteristics. Furthermore, our multi-resolution analysis gives users information about the relative potential of the clusters and their hierarchical relationship. The effectiveness of the proposed method is illustrated in three biomolecules: alanine dipeptide, Villin headpiece, and the FiP35 WW domain. PMID:23565139

Retinal Ligand Mobility Explains Internal Hydration and Reconciles Active Rhodopsin Structures

PubMed Central

Leioatts, Nicholas; Mertz, Blake; Martínez-Mayorga, Karina; Romo, Tod D.; Pitman, Michael C.; Feller, Scott E.; Grossfield, Alan; Brown, Michael F.

2014-01-01

Rhodopsin, the mammalian dim-light receptor, is one of the best-characterized G-protein-coupled receptors, a pharmaceutically important class of membrane proteins that has garnered a great deal of attention because of the recent availability of structural information. Yet the mechanism of rhodopsin activation is not fully understood. Here, we use microsecond-scale all-atom molecular dynamics simulations, validated by solid-state 2H nuclear magnetic resonance spectroscopy, to understand the transition between the dark and metarhodopsin I (Meta I) states. Our analysis of these simulations reveals striking differences in ligand flexibility between the two states. Retinal is much more dynamic in Meta I, adopting an elongated conformation similar to that seen in the recent activelike crystal structures. Surprisingly, this elongation corresponds to both a dramatic influx of bulk water into the hydrophobic core of the protein and a concerted transition in the highly conserved Trp2656.48 residue. In addition, enhanced ligand flexibility upon light activation provides an explanation for the different retinal orientations observed in X-ray crystal structures of active rhodopsin. PMID:24328554

Environment and initial state engineered dynamics of quantum and classical correlations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Cheng-Zhi, E-mail: czczwang@outlook.com; Li, Chun-Xian; Guo, Yu

Based on an open exactly solvable system coupled to an environment with nontrivial spectral density, we connect the features of quantum and classical correlations with some features of the environment, initial states of the system, and the presence of initial system–environment correlations. Some interesting features not revealed before are observed by changing the structure of environment, the initial states of system, and the presence of initial system–environment correlations. The main results are as follows. (1) Quantum correlations exhibit temporary freezing and permanent freezing even at high temperature of the environment, for which the necessary and sufficient conditions are given bymore » three propositions. (2) Quantum correlations display a transition from temporary freezing to permanent freezing by changing the structure of environment. (3) Quantum correlations can be enhanced all the time, for which the condition is put forward. (4) The one-to-one dependency relationship between all kinds of dynamic behaviors of quantum correlations and the initial states of the system as well as environment structure is established. (5) In the presence of initial system–environment correlations, quantum correlations under local environment exhibit temporary multi-freezing phenomenon. While under global environment they oscillate, revive, and damp, an explanation for which is given. - Highlights: • Various interesting behaviors of quantum and classical correlations are observed in an open exactly solvable model. • The important effects of the bath structure on quantum and classical correlations are revealed. • The one-to-one correspondence between the type of dynamical behavior of quantum discord and the initial state is given. • Quantum correlations are given in the presence of initial qubits–bath correlations.« less

An ab initio study of the structure and atomic transport in bulk liquid Ag and its liquid-vapor interface

NASA Astrophysics Data System (ADS)

del Rio, Beatriz G.; González, David J.; González, Luis E.

2016-10-01

Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals propagating excitations whose dispersion at long wavelengths is compatible with the experimental sound velocity. Results are also reported for other transport coefficients. Additional simulations have also been performed so as to study the structure of the free liquid surface. The calculated longitudinal ionic density profile shows an oscillatory behaviour, whose properties are analyzed through macroscopic and microscopic methods. The intrinsic X-ray reflectivity of the surface is predicted to show a layering peak associated to the interlayer distance.

MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.

PubMed

Sharma, Monika; Bulusu, Gopalakrishnan; Mitra, Abhijit

2009-09-01

Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-free (OPEN) state. Root-mean-square deviation, root-mean-square fluctuation, dynamic cross-correlation, and backbone torsion angle analyses are carried out on the two trajectories. These, along with solvent accessible surface area analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hitherto unreported, noncanonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.

Slush-like polar structures in single-crystal relaxors

NASA Astrophysics Data System (ADS)

Takenaka, Hiroyuki; Grinberg, Ilya; Liu, Shi; Rappe, Andrew M.

2017-06-01

Despite more than 50 years of investigation, it is still unclear how the underlying structure of relaxor ferroelectrics gives rise to their defining properties, such as ultrahigh piezoelectric coefficients, high permittivity over a broad temperature range, diffuse phase transitions, strong frequency dependence in dielectric response, and phonon anomalies. The model of polar nanoregions inside a non-polar matrix has been widely used to describe the structure of relaxor ferroelectrics. However, the lack of precise knowledge about the shapes, growth and dipole patterns of polar nanoregions has led to the characterization of relaxors as “hopeless messes”, and no predictive model for relaxor behaviour is currently available. Here we use molecular dynamics simulations of the prototypical Pb(Mg1/3,Nb2/3)O3-PbTiO3 relaxor material to examine its structure and the spatial and temporal polarization correlations. Our simulations show that the unusual properties of relaxors stem from the presence of a multi-domain state with extremely small domain sizes (2-10 nanometres), and no non-polar matrix, owing to the local dynamics. We find that polar structures in the multi-domain state in relaxors are analogous to those of the slush state of water. The multi-domain structure of relaxors that is revealed by our molecular dynamics simulations is consistent with recent experimental diffuse scattering results and indicates that relaxors have a high density of low-angle domain walls. This insight explains the recently discovered classes of relaxors that cannot be described by the polar nanoregion model, and provides guidance for the design and synthesis of new relaxor materials.

Insight into the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corradini, Dario; Vuilleumier, Rodolphe, E-mail: rodolphe.vuilleumier@ens.fr; Sorbonne Universités, UPMC Univ. Paris 06, PASTEUR, 75005 Paris

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900–1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, wemore » present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture’s self-diffusion coefficients, viscosity, and ionic conductivity.« less

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu; Yang, Mo

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heatmore » transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.« less

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Applications of solid-state NMR to membrane proteins.

PubMed

Ladizhansky, Vladimir

2017-11-01

Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: all-atom molecular dynamics simulations.

PubMed

Yamane, Tsutomu; Murakami, Satoshi; Ikeguchi, Mitsunori

2013-10-29

The multidrug transporter AcrB actively exports a wide variety of noxious compounds using proton-motive force as an energy source in Gram-negative bacteria. AcrB adopts an asymmetric structure comprising three protomers with different conformations that are sequentially converted during drug export; these cyclic conformational changes during drug export are referred to as functional rotation. To investigate functional rotation driven by proton-motive force, all-atom molecular dynamics simulations were performed. Using different protonation states for the titratable residues in the middle of the transmembrane domain, our simulations revealed the correlation between the specific protonation states and the side-chain configurations. Changing the protonation state for Asp408 induced a spontaneous structural transition, which suggests that the proton translocation stoichiometry may be one proton per functional rotation cycle. Furthermore, our simulations demonstrate that alternating the protonation states in the transmembrane domain induces functional rotation in the porter domain, which is primarily responsible for drug transport.

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Vulnerability of dynamic systems

NASA Technical Reports Server (NTRS)

Siljak, D. D.

1976-01-01

Directed graphs are associated with dynamic systems in order to determine in any given system if each state can be reached by at least one input (input reachability), or can each state reach at least one output (output reachability). Then, the structural perturbations of a dynamic system are identified as lines or points removals from the corresponding digraph, and a system is considered vulnerable at those lines or points of the digraph whose removal destroys its input or output reachability. A suitable framework is formulated for resolving the problems of reachability and vulnerability which applies to both linear and nonlinear systems alike.

A network of molecular switches controls the activation of the two-component response regulator NtrC

NASA Astrophysics Data System (ADS)

Vanatta, Dan K.; Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S.

2015-06-01

Recent successes in simulating protein structure and folding dynamics have demonstrated the power of molecular dynamics to predict the long timescale behaviour of proteins. Here, we extend and improve these methods to predict molecular switches that characterize conformational change pathways between the active and inactive state of nitrogen regulatory protein C (NtrC). By employing unbiased Markov state model-based molecular dynamics simulations, we construct a dynamic picture of the activation pathways of this key bacterial signalling protein that is consistent with experimental observations and predicts new mutants that could be used for validation of the mechanism. Moreover, these results suggest a novel mechanistic paradigm for conformational switching.

Influence of backup bearings and support structure dynamics on the behavior of rotors with active supports

NASA Technical Reports Server (NTRS)

Flowers, George T.

1995-01-01

Progress made in the current year is listed, and the following papers are included in the appendix: Steady-State Dynamic Behavior of an Auxiliary Bearing Supported Rotor System; Dynamic Behavior of a Magnetic Bearing Supported Jet Engine Rotor with Auxiliary Bearings; Dynamic Modelling and Response Characteristics of a Magnetic Bearing Rotor System with Auxiliary Bearings; and Synchronous Dynamics of a Coupled Shaft/Bearing/Housing System with Auxiliary Support from a Clearance Bearing: Analysis and Experiment.

Autonomous learning by simple dynamical systems with delayed feedback.

PubMed

Kaluza, Pablo; Mikhailov, Alexander S

2014-09-01

A general scheme for the construction of dynamical systems able to learn generation of the desired kinds of dynamics through adjustment of their internal structure is proposed. The scheme involves intrinsic time-delayed feedback to steer the dynamics towards the target performance. As an example, a system of coupled phase oscillators, which can, by changing the weights of connections between its elements, evolve to a dynamical state with the prescribed (low or high) synchronization level, is considered and investigated.

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

PubMed

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

2015-10-01

The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.

Inner-shell excitation and ionic fragmentation of molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hitchcock, A.P.; Tyliszczak, T.; Cavell, R.G.

1997-04-01

Inner-shell excitation and associated decay spectroscopies are site specific probes of electronic and geometrical structure and photoionization dynamics. X-ray absorption probes the geometric and electronic structure, while time-of-flight mass spectrometry with multi-coincidence detection provides information on the photofragmentation dynamics of the initially produced inner-shell state. Auger decay of inner-shell excited and ionised states is an efficient source of multiply charged ions. The charge separation and fragmentation of these species, studied by photoelectron-photoion-photoion coincidence (also called charge separation mass spectrometry) gives insights into bonding and electronic structure. In molecules, the dependence of the fragmentation process on the X-ray energy can revealmore » cases of site and/or state selective fragmentation. At the ALS the authors have examined the soft X-ray spectroscopy and ionic fragmentation of a number of molecules, including carboranes, silylenes, phosphorus halides, SF{sub 6} and CO{sub 2}. Their work is illustrated using results from the carborane and PF{sub 3} studies.« less

Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization

PubMed Central

2018-01-01

Macrocycles are of considerable interest as highly specific drug candidates, yet they challenge standard conformer generators with their large number of rotatable bonds and conformational restrictions. Here, we present a molecular dynamics-based routine that bypasses current limitations in conformational sampling and extensively profiles the free energy landscape of peptidic macrocycles in solution. We perform accelerated molecular dynamics simulations to capture a diverse conformational ensemble. By applying an energetic cutoff, followed by geometric clustering, we demonstrate the striking robustness and efficiency of the approach in identifying highly populated conformational states of cyclic peptides. The resulting structural and thermodynamic information is benchmarked against interproton distances from NMR experiments and conformational states identified by X-ray crystallography. Using three different model systems of varying size and flexibility, we show that the method reliably reproduces experimentally determined structural ensembles and is capable of identifying key conformational states that include the bioactive conformation. Thus, the described approach is a robust method to generate conformations of peptidic macrocycles and holds promise for structure-based drug design. PMID:29652495

Interfacing the Ab initio multiple spawning method with electronic structure methods in GAMESS: Photodecay of trans-Azomethane

DOE PAGES

Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; ...

2014-10-20

This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitationmore » on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.« less

Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.

PubMed

Kamenik, Anna S; Lessel, Uta; Fuchs, Julian E; Fox, Thomas; Liedl, Klaus R

2018-05-29

Macrocycles are of considerable interest as highly specific drug candidates, yet they challenge standard conformer generators with their large number of rotatable bonds and conformational restrictions. Here, we present a molecular dynamics-based routine that bypasses current limitations in conformational sampling and extensively profiles the free energy landscape of peptidic macrocycles in solution. We perform accelerated molecular dynamics simulations to capture a diverse conformational ensemble. By applying an energetic cutoff, followed by geometric clustering, we demonstrate the striking robustness and efficiency of the approach in identifying highly populated conformational states of cyclic peptides. The resulting structural and thermodynamic information is benchmarked against interproton distances from NMR experiments and conformational states identified by X-ray crystallography. Using three different model systems of varying size and flexibility, we show that the method reliably reproduces experimentally determined structural ensembles and is capable of identifying key conformational states that include the bioactive conformation. Thus, the described approach is a robust method to generate conformations of peptidic macrocycles and holds promise for structure-based drug design.

Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S{sub 1} states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Álvarez-Valtierra, Leonardo, E-mail: leoav@fisica.ugto.mx, E-mail: gmerino@mda.cinvestav.mx

2015-09-07

The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, butmore » it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent   –OH and   –OCH{sub 3} groups plays a major role in these dynamics.« less

Spatial Patterns in Alternative States and Thresholds: A Missing Link for Management of Landscapes?

USDA-ARS?s Scientific Manuscript database

The detection of threshold dynamics (and other dynamics of interest) would benefit from explicit representations of spatial patterns of disturbance, spatial dependence in responses to disturbance, and the spatial structure of feedbacks in the design of monitoring and management strategies. Spatially...

The analysis of dynamic characteristics and wind-induced displacement response of space Beam String Structure

NASA Astrophysics Data System (ADS)

Chen, Yong Jian; Feng, Zhen Fa; Qi, Ai; Huang, Ying

2018-06-01

The Beam String Structure structural system, also called BSS, has the advantages of lighter dead weight and greater flexibility. The wind load is the main design control factor. The dynamic characteristics and wind-induced displacement response of BSS are studied by the finite element method. The roof structure of the stadium roof of the Fuzhou Olympic Sports Center is the engineering background. 1)The numerical model was built by ANSYS, by shape finding, determine the initial stress state of structural members such as external cables; 2)From the analysis of dynamic characteristics, the main mode of vibration is the vibration of cables; 3)The wind speed spectrum of MATLAB generation structure is obtained by AR method, the structural response of the structure under static wind load and fluctuating wind load is calculated. From the analysis result, considering the equivalent static wind load of BSS , the design of adverse wind is not safe, and the fluctuating wind load should be taken into account.

Can Structural Optimization Explain Slow Dynamics of Rocks?

NASA Astrophysics Data System (ADS)

Kim, H.; Vistisen, O.; Tencate, J. A.

2009-12-01

Slow dynamics is a recovery process that describes the return to an equilibrium state after some external energy input is applied and then removed. Experimental studies on many rocks have shown that a modest acoustic energy input results in slow dynamics. The recovery process of the stiffness has consistently been found to be linear to log(time) for a wide range of geomaterials and the time constants appear to be unique to the material [TenCate JA, Shankland TJ (1996), Geophys Res Lett 23, 3019-3022]. Measurements of this nonequilibrium effect in rocks (e.g. sandstones and limestones) have been linked directly to the cement holding the individual grains together [Darling TW, TenCate JA, Brown DW, Clausen B, Vogel SC (2004), Geophys Res Lett 31, L16604], also suggesting a potential link to porosity and permeability. Noting that slow dynamics consistently returns the overall stiffness of rocks to its maximum (original) state, it is hypothesized that the original state represents the global minimum strain energy state. Consequently the slow dynamics process represents the global minimization or optimization process. Structural optimization, which has been developed for engineering design, minimises the total strain energy by rearranging the material distribution [Kim H, Querin OM, Steven GP, Xie YM (2002), Struct Multidiscip Optim 24, 441-448]. The optimization process effectively rearranges the way the material is cemented. One of the established global optimization methods is simulated annealing (SA). Derived from cooling of metal to a thermal equilibrium, SA finds an optimum solution by iteratively moving the system towards the minimum energy state with a probability of 'uphill' moves. It has been established that the global optimum can be guaranteed by applying a log(time) linear cooling schedule [Hajek B (1988, Math Ops Res, 15, 311-329]. This work presents the original study of applying SA to the maximum stiffness optimization problem. Preliminary results indicate that the maximum stiffness solutions are achieved when using log(time) linear cooling schedule. The optimization history reveals that the overall stiffness of the structure is increased linearly to log(time). The results closely resemble the slow dynamics stiffness recovery of geomaterials and support the hypothesis that the slow dynamics is an optimization process for strain energy. [Work supported by the Department of Energy through the LANL/LDRD Program].

Multivariate dynamical modelling of structural change during development.

PubMed

Ziegler, Gabriel; Ridgway, Gerard R; Blakemore, Sarah-Jayne; Ashburner, John; Penny, Will

2017-02-15

Here we introduce a multivariate framework for characterising longitudinal changes in structural MRI using dynamical systems. The general approach enables modelling changes of states in multiple imaging biomarkers typically observed during brain development, plasticity, ageing and degeneration, e.g. regional gray matter volume of multiple regions of interest (ROIs). Structural brain states follow intrinsic dynamics according to a linear system with additional inputs accounting for potential driving forces of brain development. In particular, the inputs to the system are specified to account for known or latent developmental growth/decline factors, e.g. due to effects of growth hormones, puberty, or sudden behavioural changes etc. Because effects of developmental factors might be region-specific, the sensitivity of each ROI to contributions of each factor is explicitly modelled. In addition to the external effects of developmental factors on regional change, the framework enables modelling and inference about directed (potentially reciprocal) interactions between brain regions, due to competition for space, or structural connectivity, and suchlike. This approach accounts for repeated measures in typical MRI studies of development and aging. Model inversion and posterior distributions are obtained using earlier established variational methods enabling Bayesian evidence-based comparisons between various models of structural change. Using this approach we demonstrate dynamic cortical changes during brain maturation between 6 and 22 years of age using a large openly available longitudinal paediatric dataset with 637 scans from 289 individuals. In particular, we model volumetric changes in 26 bilateral ROIs, which cover large portions of cortical and subcortical gray matter. We account for (1) puberty-related effects on gray matter regions; (2) effects of an early transient growth process with additional time-lag parameter; (3) sexual dimorphism by modelling parameter differences between boys and girls. There is evidence that the regional pattern of sensitivity to dynamic hidden growth factors in late childhood is similar across genders and shows a consistent anterior-posterior gradient with strongest impact to prefrontal cortex (PFC) brain changes. Finally, we demonstrate the potential of the framework to explore the coupling of structural changes across a priori defined subnetworks using an example of previously established resting state functional connectivity. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The structure of neuronal calcium sensor-1 in solution revealed by molecular dynamics simulations.

PubMed

Bellucci, Luca; Corni, Stefano; Di Felice, Rosa; Paci, Emanuele

2013-01-01

Neuronal calcium sensor-1 (NCS-1) is a protein able to trigger signal transduction processes by binding a large number of substrates and re-shaping its structure depending on the environmental conditions. The X-ray crystal structure of the unmyristoilated NCS-1 shows a large solvent-exposed hydrophobic crevice (HC); this HC is partially occupied by the C-terminal tail and thus elusive to the surrounding solvent. We studied the native state of NCS-1 by performing room temperature molecular dynamics (MD) simulations starting from the crystal and the solution structures. We observe relaxation to a state independent of the initial structure, in which the C-terminal tail occupies the HC. We suggest that the C-terminal tail shields the HC binding pocket and modulates the affinity of NCS-1 for its natural targets. By analyzing the topology and nature of the inter-residue potential energy, we provide a compelling description of the interaction network that determines the three-dimensional organization of NCS-1.

Several routes to the glassy states in the one component soft core system: revisited by molecular dynamics.

PubMed

Habasaki, Junko; Ueda, Akira

2011-02-28

Molecular dynamics simulations have been performed to study the glass transition for the soft core system with a pair potential φ(n)(r) = ε(σ∕r)(n) of n = 12. Using the compressibility factor, PV/Nk(B)T=P̃(ρ*), its phase diagram can be represented as a function of a reduced density, ρ∗ = ρ(ε∕k(B)T)(3∕n), where ρ = Nσ(3)∕V. In the present work, NVE relaxations to the glassy or crystalline states starting from the unstable states in the phase diagram have been revisited in details and compared with other processes. Relaxation processes can be characterized by the time dependence of the dynamical compressibility factor (PV/Nk(B)T)(t) (≡g(ρ(t)*)) on the phase diagram. In some cases, g(ρ(t)*) reached a crystal branch in the phase diagram; however, metastable states are found in many cases. With connecting points for the metastable states in the phase diagram, we can define a glass branch where the dynamics of particles are almost frozen. The structures observed there have common properties characterized as glasses. Although overlaps of glass forming process and nanocrystallization process are observed in some cases, these behaviors are distinguishable to each other by the characteristics of structures. There are several routes to the glass branch and we suggest that all of them are the glass transition.

Ultrafast dynamics of multi-exciton state coupled to coherent vibration in zinc chlorin aggregates for artificial photosynthesis.

PubMed

Shi, Tongchao; Liu, Zhengzheng; Miyatake, Tomohiro; Tamiaki, Hitoshi; Kobayashi, Takayoshi; Zhang, Zeyu; Du, Juan; Leng, Yuxin

2017-11-27

Ultrafast vibronic dynamics induced by the interaction of the Frenkel exciton with the coherent molecular vibrations in a layer-structured zinc chlorin aggregates prepared for artificial photosynthesis have been studied by 7.1 fs real-time vibrational spectroscopy with multi-spectrum detection. The fast decay of 100 ± 5fs is ascribed to the relaxation from the higher multi-exciton state (MES) to the one-exciton state, and the slow one of 863 ± 70fs is assigned to the relaxation from Q-exciton state to the dark nonfluorescent charge-transfer (CT) state, respectively. In addition, the wavelength dependences of the exciton-vibration coupling strength are found to follow the zeroth derivative of the transient absorption spectra of the exciton. It could be explained in term of the transition dipole moment modulated by dynamic intensity borrowing between the B transition and the Q transition through the vibronic interactions.

The engine of microtubule dynamics comes into focus.

PubMed

Mitchison, T J

2014-05-22

In this issue, Alushin et al. report high-resolution structures of three states of the microtubule lattice: GTP-bound, which is stable to depolymerization; unstable GDP-bound; and stable Taxol and GDP-bound. By comparing these structures at near-atomic resolution, they are able to propose a detailed model for how GTP hydrolysis destabilizes the microtubule and thus powers dynamic instability and chromosome movement. Destabilization of cytoskeleton filaments by nucleotide hydrolysis is an important general principle in cell dynamics, and this work represents a major step forward on a problem with a long history. Copyright © 2014 Elsevier Inc. All rights reserved.

Multiple dynamic regimes in colloid-polymer dispersions: New insight using X-ray photon correlation spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Srivastava, Sunita; Kishore, Suhasini; Narayanan, Suresh

We present an X-ray photon correlation spectros- copy (XPCS) study of dynamic transitions in an anisotropic colloid-polymer dispersion with multiple arrested states. The results provide insight into the mechanism for formation of repulsive glasses, attractive glasses, and networked gels of col- loids with weakly adsorbing polymer chains. In the presence of adsorbing polymer chains, we observe three distinct regimes: a state with slow dynamics consisting of finite particles and clusters, for which interparticle interactions are predominantly repulsive; a second dynamic regime occurring above the satu- ration concentration of added polymer, in which small clusters of nanoparticles form via a short-rangemore » depletion attraction; and a third regime above the overlap concentration in which dynamics of clusters are independent of polymer chain length. The observed complex dynamic state diagram is primarily gov- erned by the structural reorganization of a nanoparticle cluster and polymer chains at the nanoparticle-polymer surface and in the concentrated medium, which in turn controls the dynamics of the dispersion« less

Dynamics of coherent states in regular and chaotic regimes of the non-integrable Dicke model

NASA Astrophysics Data System (ADS)

Lerma-Hernández, S.; Chávez-Carlos, J.; Bastarrachea-Magnani, M. A.; López-del-Carpio, B.; Hirsch, J. G.

2018-04-01

The quantum dynamics of initial coherent states is studied in the Dicke model and correlated with the dynamics, regular or chaotic, of their classical limit. Analytical expressions for the survival probability, i.e. the probability of finding the system in its initial state at time t, are provided in the regular regions of the model. The results for regular regimes are compared with those of the chaotic ones. It is found that initial coherent states in regular regions have a much longer equilibration time than those located in chaotic regions. The properties of the distributions for the initial coherent states in the Hamiltonian eigenbasis are also studied. It is found that for regular states the components with no negligible contribution are organized in sequences of energy levels distributed according to Gaussian functions. In the case of chaotic coherent states, the energy components do not have a simple structure and the number of participating energy levels is larger than in the regular cases.

Propagating stress-pulses and wiggling transition revealed in string dynamics

NASA Astrophysics Data System (ADS)

Yao, Zhenwei

2018-02-01

Understanding string dynamics yields insights into the intricate dynamic behaviors of various filamentary thin structures in nature and industry covering multiple length scales. In this work, we investigate the planar dynamics of a flexible string where one end is free and the other end is subject to transverse and longitudinal motions. Under transverse harmonic motion, we reveal the propagating pulse structure in the stress profile over the string, and analyze its role in bringing the system into a chaotic state. For a string where one end is under longitudinal uniform acceleration, we identify the wiggling transition, derive the analytical wiggling solution from the string equations, and present the phase diagram.

Dynamic properties of epidemic spreading on finite size complex networks

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Yang; Shan, Xiu-Ming; Ren, Yong; Jiao, Jian; Qiu, Ben

2005-11-01

The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptible-infected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.

The endoplasmic reticulum: structure, function and response to cellular signaling.

PubMed

Schwarz, Dianne S; Blower, Michael D

2016-01-01

The endoplasmic reticulum (ER) is a large, dynamic structure that serves many roles in the cell including calcium storage, protein synthesis and lipid metabolism. The diverse functions of the ER are performed by distinct domains; consisting of tubules, sheets and the nuclear envelope. Several proteins that contribute to the overall architecture and dynamics of the ER have been identified, but many questions remain as to how the ER changes shape in response to cellular cues, cell type, cell cycle state and during development of the organism. Here we discuss what is known about the dynamics of the ER, what questions remain, and how coordinated responses add to the layers of regulation in this dynamic organelle.

Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants.

PubMed

Mou, Yun; Huang, Po-Ssu; Thomas, Leonard M; Mayo, Stephen L

2015-08-14

In standard implementations of computational protein design, a positive-design approach is used to predict sequences that will be stable on a given backbone structure. Possible competing states are typically not considered, primarily because appropriate structural models are not available. One potential competing state, the domain-swapped dimer, is especially compelling because it is often nearly identical with its monomeric counterpart, differing by just a few mutations in a hinge region. Molecular dynamics (MD) simulations provide a computational method to sample different conformational states of a structure. Here, we tested whether MD simulations could be used as a post-design screening tool to identify sequence mutations leading to domain-swapped dimers. We hypothesized that a successful computationally designed sequence would have backbone structure and dynamics characteristics similar to that of the input structure and that, in contrast, domain-swapped dimers would exhibit increased backbone flexibility and/or altered structure in the hinge-loop region to accommodate the large conformational change required for domain swapping. While attempting to engineer a homodimer from a 51-amino-acid fragment of the monomeric protein engrailed homeodomain (ENH), we had instead generated a domain-swapped dimer (ENH_DsD). MD simulations on these proteins showed increased B-factors derived from MD simulation in the hinge loop of the ENH_DsD domain-swapped dimer relative to monomeric ENH. Two point mutants of ENH_DsD designed to recover the monomeric fold were then tested with an MD simulation protocol. The MD simulations suggested that one of these mutants would adopt the target monomeric structure, which was subsequently confirmed by X-ray crystallography. Copyright © 2015. Published by Elsevier Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jianping, E-mail: jwang@iccas.ac.cn; Yang, Fan; Zhao, Juan

In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH{sub 3}CN, CHCl{sub 3}, and CCl{sub 4}), were examined using the N—H stretching vibration (or the amide-A mode) as a structural probe. Steady-state and transient infrared spectroscopic methods in combination with quantum chemical computations and molecular dynamics simulations were used. It was found that in these solvents, NEPA exists in different aggregation forms, including monomer, dimer, and oligomers. Hydrogen-bonding interaction and local-solvent environment both affect the amide-A absorption profile and its vibrational relaxation dynamics and also affect the structural dynamics ofmore » NEPA. In particular, a correlation between the red-shifted frequency for the NEPA monomer from nonpolar to polar solvent and the vibrational excitation relaxation rate of the N—H stretching mode was observed.« less

Path integral molecular dynamic simulation of flexible molecular systems in their ground state: Application to the water dimer

NASA Astrophysics Data System (ADS)

Schmidt, Matthew; Roy, Pierre-Nicholas

2018-03-01

We extend the Langevin equation Path Integral Ground State (LePIGS), a ground state quantum molecular dynamics method, to simulate flexible molecular systems and calculate both energetic and structural properties. We test the approach with the H2O and D2O monomers and dimers. We systematically optimize all simulation parameters and use a unity trial wavefunction. We report ground state energies, dissociation energies, and structural properties using three different water models, two of which are empirically based, q-TIP4P/F and q-SPC/Fw, and one which is ab initio, MB-pol. We demonstrate that our energies calculated from LePIGS can be merged seamlessly with low temperature path integral molecular dynamics calculations and note the similarities between the two methods. We also benchmark our energies against previous diffusion Monte Carlo calculations using the same potentials and compare to experimental results. We further demonstrate that accurate vibrational energies of the H2O and D2O monomer can be calculated from imaginary time correlation functions generated from the LePIGS simulations using solely the unity trial wavefunction.

New open conformation of SMYD3 implicates conformational selection and allostery

PubMed Central

Spellmon, Nicholas; Sun, Xiaonan; Xue, Wen; Holcomb, Joshua; Chakravarthy, Srinivas; Shang, Weifeng; Edwards, Brian; Sirinupong, Nualpun; Li, Chunying; Yang, Zhe

2016-01-01

SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD). The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation. PMID:28050603

The Design, Synthesis, and Study of Solid-State Molecular Rotors: Structure/Function Relationships for Condensed-Phase Anisotropic Dynamics

NASA Astrophysics Data System (ADS)

Vogelsberg, Cortnie Sue

Amphidynamic crystals are an extremely promising platform for the development of artificial molecular machines and stimuli-responsive materials. In analogy to skeletal muscle, their function will rely upon the collective operation of many densely packed molecular machines (i.e. actin-bound myosin) that are self-assembled in a highly organized anisotropic medium. By choosing lattice-forming elements and moving "parts" with specific functionalities, individual molecular machines may be synthesized and self-assembled in order to carry out desirable functions. In recent years, efforts in the design of amphidynamic materials based on molecular gyroscopes and compasses have shown that a certain amount of free volume is essential to facilitate internal rotation and reorientation within a crystal. In order to further establish structure/function relationships to advance the development of increasingly complex molecular machinery, molecular rotors and a molecular "spinning" top were synthesized and incorporated into a variety of solid-state architectures with different degrees of periodicity, dimensionality, and free volume. Specifically, lamellar molecular crystals, hierarchically ordered periodic mesoporous organosilicas, and metal-organic frameworks were targeted for the development of solid-state molecular machines. Using an array of solid-state nuclear magnetic resonance spectroscopy techniques, the dynamic properties of these novel molecular machine assemblies were determined and correlated with their corresponding structural features. It was found that architecture type has a profound influence on functional dynamics. The study of layered molecular crystals, composed of either molecular rotors or "spinning" tops, probed functional dynamics within dense, highly organized environments. From their study, it was discovered that: 1) crystallographically distinct sites may be utilized to differentiate machine function, 2) halogen bonding interactions are sufficiently strong to direct an assembly of molecular machines, 3) the relative flexibility of the crystal environment proximate to a dynamic component may have a significant effect on its function, and, 4) molecular machines, which possess both solid-state photochemical reactivity and dynamics may show complex reaction kinetics if the correlation time of the dynamic process and the lifetime of the excited state occur on the same time scale and the dynamic moiety inherently participates as a reaction intermediate. The study of periodic mesoporous organosilica with hierarchical order probed molecular dynamics within 2D layers of molecular rotors, organized in only one dimension and with ca. 50% exposed to the mesopore free volume. From their study, it was discovered that: 1) molecular rotors, which comprise the layers of the mesopore walls, form a 2D rotational glass, 2) rotator dynamics within the 2D rotational glass undergo a transition to a 2D rotational fluid, and, 3) a 2D rotational glass transition may be exploited to develop hyper-sensitive thermally activated molecular machines. The study of a metal-organic framework assembled from molecular rotors probed dynamics in a periodic three-dimensional free-volume environment, without the presence of close contacts. From the study of this solid-state material, it was determined that: 1) the intrinsic electronic barrier is one of the few factors, which may affect functional dynamics in a true free-volume environment, and, 2) molecular machines with dynamic barriers <

Hysteresis, reentrance, and glassy dynamics in systems of self-propelled rods

NASA Astrophysics Data System (ADS)

Kuan, Hui-Shun; Blackwell, Robert; Hough, Loren E.; Glaser, Matthew A.; Betterton, M. D.

2015-12-01

Nonequilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studied high-aspect-ratio self-propelled rods over a wide range of packing fractions and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state, the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluidlike behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition that, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped micro-organisms.

Hysteresis, reentrance, and glassy dynamics in systems of self-propelled rods.

PubMed

Kuan, Hui-Shun; Blackwell, Robert; Hough, Loren E; Glaser, Matthew A; Betterton, M D

2015-01-01

Nonequilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studied high-aspect-ratio self-propelled rods over a wide range of packing fractions and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state, the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluidlike behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition that, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped micro-organisms.

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.

Microsecond protein dynamics observed at the single-molecule level

PubMed Central

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

Achieving Optimal Self-Adaptivity for Dynamic Tuning of Organic Semiconductors through Resonance Engineering.

PubMed

Tao, Ye; Xu, Lijia; Zhang, Zhen; Chen, Runfeng; Li, Huanhuan; Xu, Hui; Zheng, Chao; Huang, Wei

2016-08-03

Current static-state explorations of organic semiconductors for optimal material properties and device performance are hindered by limited insights into the dynamically changed molecular states and charge transport and energy transfer processes upon device operation. Here, we propose a simple yet successful strategy, resonance variation-based dynamic adaptation (RVDA), to realize optimized self-adaptive properties in donor-resonance-acceptor molecules by engineering the resonance variation for dynamic tuning of organic semiconductors. Organic light-emitting diodes hosted by these RVDA materials exhibit remarkably high performance, with external quantum efficiencies up to 21.7% and favorable device stability. Our approach, which supports simultaneous realization of dynamically adapted and selectively enhanced properties via resonance engineering, illustrates a feasible design map for the preparation of smart organic semiconductors capable of dynamic structure and property modulations, promoting the studies of organic electronics from static to dynamic.

Preparation and Relaxation of Very Stable Glassy States of a Simulated Liquid

NASA Astrophysics Data System (ADS)

Jack, Robert L.; Hedges, Lester O.; Garrahan, Juan P.; Chandler, David

2011-12-01

We prepare metastable glassy states in a model glass former made of Lennard-Jones particles by sampling biased ensembles of trajectories with low dynamical activity. These trajectories form an inactive dynamical phase whose “fast” vibrational degrees of freedom are maintained at thermal equilibrium by contact with a heat bath, while the “slow” structural degrees of freedom are located in deep valleys of the energy landscape. We examine the relaxation to equilibrium and the vibrational properties of these metastable states. The glassy states we prepare by our trajectory sampling method are very stable to thermal fluctuations and also more mechanically rigid than low-temperature equilibrated configurations.

Topological Properties and the Dynamical Crossover from Mixed-Valence to Kondo-Lattice Behavior in the Golden Phase of SmS.

PubMed

Kang, Chang-Jong; Choi, Hong Chul; Kim, Kyoo; Min, B I

2015-04-24

We have investigated temperature-dependent behaviors of electronic structure and resistivity in a mixed-valent golden phase of SmS, based on the dynamical mean-field-theory band-structure calculations. Upon cooling, the coherent Sm 4f bands are formed to produce the hybridization-induced pseudogap near the Fermi level, and accordingly the topology of the Fermi surface is changed to exhibit a Lifshitz-like transition. The surface states emerging in the bulk gap region are found to be not topologically protected states but just typical Rashba spin-polarized states, indicating that SmS is not a topological Kondo semimetal. From the analysis of anomalous resistivity behavior in SmS, we have identified universal energy scales, which characterize the Kondo-mixed-valent semimetallic systems.

Controllability of structural brain networks

NASA Astrophysics Data System (ADS)

Gu, Shi; Pasqualetti, Fabio; Cieslak, Matthew; Telesford, Qawi K.; Yu, Alfred B.; Kahn, Ari E.; Medaglia, John D.; Vettel, Jean M.; Miller, Michael B.; Grafton, Scott T.; Bassett, Danielle S.

2015-10-01

Cognitive function is driven by dynamic interactions between large-scale neural circuits or networks, enabling behaviour. However, fundamental principles constraining these dynamic network processes have remained elusive. Here we use tools from control and network theories to offer a mechanistic explanation for how the brain moves between cognitive states drawn from the network organization of white matter microstructure. Our results suggest that densely connected areas, particularly in the default mode system, facilitate the movement of the brain to many easily reachable states. Weakly connected areas, particularly in cognitive control systems, facilitate the movement of the brain to difficult-to-reach states. Areas located on the boundary between network communities, particularly in attentional control systems, facilitate the integration or segregation of diverse cognitive systems. Our results suggest that structural network differences between cognitive circuits dictate their distinct roles in controlling trajectories of brain network function.

Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase.

PubMed

Pemberton, Ryan P; Ho, Krystina C; Tantillo, Dean J

2015-04-01

The relative importance of preorganization, selective transition state stabilization and inherent reactivity are assessed through quantum chemical and docking calculations for a sesquiterpene synthase ( epi -isozizaene synthase, EIZS). Inherent reactivity of the bisabolyl cation, both static and dynamic, appears to determine the pathway to product, although preorganization and selective binding of the final transition state structure in the multi-step carbocation cascade that forms epi -isozizaene appear to play important roles.

Microprocessor based implementation of attitude and shape control of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.

1984-01-01

The feasibility of off the shelf eight bit and 16 bit microprocessors to implement linear state variable feedback control laws and assessing the real time response to spacecraft dynamics is studied. The complexity of the dynamic model is described along with the appropriate software. An experimental setup of a beam, microprocessor system for implementing the control laws and the needed generalized software to implement any state variable feedback control system is included.

Nonlinear dynamics of solitary and optically injected two-element laser arrays with four different waveguide structures: a numerical study.

PubMed

Li, Nianqiang; Susanto, H; Cemlyn, B R; Henning, I D; Adams, M J

2018-02-19

We study the nonlinear dynamics of solitary and optically injected two-element laser arrays with a range of waveguide structures. The analysis is performed with a detailed direct numerical simulation, where high-resolution dynamic maps are generated to identify regions of dynamic instability in the parameter space of interest. Our combined one- and two-parameter bifurcation analysis uncovers globally diverse dynamical regimes (steady-state, oscillation, and chaos) in the solitary laser arrays, which are greatly influenced by static design waveguiding structures, the amplitude-phase coupling factor of the electric field, i.e. the linewidth-enhancement factor, as well as the control parameter, e.g. the pump rate. When external optical injection is introduced to one element of the arrays, we show that the whole system can be either injection-locked simultaneously or display rich, different dynamics outside the locking region. The effect of optical injection is to significantly modify the nature and the regions of nonlinear dynamics from those found in the solitary case. We also show similarities and differences (asymmetry) between the oscillation amplitude of the two elements of the array in specific well-defined regions, which hold for all the waveguiding structures considered. Our findings pave the way to a better understanding of dynamic instability in large arrays of lasers.

Steady states and outbreaks of two-phase nonlinear age-structured model of population dynamics with discrete time delay.

PubMed

Akimenko, Vitalii; Anguelov, Roumen

2017-12-01

In this paper we study the nonlinear age-structured model of a polycyclic two-phase population dynamics including delayed effect of population density growth on the mortality. Both phases are modelled as a system of initial boundary values problem for semi-linear transport equation with delay and initial problem for nonlinear delay ODE. The obtained system is studied both theoretically and numerically. Three different regimes of population dynamics for asymptotically stable states of autonomous systems are obtained in numerical experiments for the different initial values of population density. The quasi-periodical travelling wave solutions are studied numerically for the autonomous system with the different values of time delays and for the system with oscillating death rate and birth modulus. In both cases it is observed three types of travelling wave solutions: harmonic oscillations, pulse sequence and single pulse.

Neural-network-observer-based optimal control for unknown nonlinear systems using adaptive dynamic programming

NASA Astrophysics Data System (ADS)

Liu, Derong; Huang, Yuzhu; Wang, Ding; Wei, Qinglai

2013-09-01

In this paper, an observer-based optimal control scheme is developed for unknown nonlinear systems using adaptive dynamic programming (ADP) algorithm. First, a neural-network (NN) observer is designed to estimate system states. Then, based on the observed states, a neuro-controller is constructed via ADP method to obtain the optimal control. In this design, two NN structures are used: a three-layer NN is used to construct the observer which can be applied to systems with higher degrees of nonlinearity and without a priori knowledge of system dynamics, and a critic NN is employed to approximate the value function. The optimal control law is computed using the critic NN and the observer NN. Uniform ultimate boundedness of the closed-loop system is guaranteed. The actor, critic, and observer structures are all implemented in real-time, continuously and simultaneously. Finally, simulation results are presented to demonstrate the effectiveness of the proposed control scheme.

Signatures of non-adiabatic dynamics in the fine-structure state distributions of the OH( X ˜ / A ˜ ) products in the B-band photodissociation of H2O

NASA Astrophysics Data System (ADS)

Zhou, Linsen; Xie, Daiqian; Guo, Hua

2015-03-01

A detailed quantum mechanical characterization of the photodissociation dynamics of H2O at 121.6 nm is presented. The calculations were performed using a full-dimensional wave packet method on coupled potential energy surfaces of all relevant electronic states. Our state-to-state model permits a detailed analysis of the OH( X ˜ / A ˜ ) product fine-structure populations as a probe of the non-adiabatic dissociation dynamics. The calculated rotational state distributions of the two Λ-doublet levels of OH( X ˜ , v = 0) exhibit very different characteristics. The A' states, produced mostly via the B ˜ → X ˜ conical intersection pathway, have significantly higher populations than the A″ counterparts, which are primarily from the B ˜ → A ˜ Renner-Teller pathway. The former features a highly inverted and oscillatory rotational state distribution, while the latter has a smooth distribution with much less rotational excitation. In good agreement with experiment, the calculated total OH( X ˜ ) rotational state distribution and anisotropy parameters show clear even-odd oscillations, which can be attributed to a quantum mechanical interference between waves emanating from the HOH and HHO conical intersections in the B ˜ → X ˜ non-adiabatic pathway. On the other hand, the experiment-theory agreement for the OH( A ˜ ) fragment is also satisfactory, although some small quantitative differences suggest remaining imperfections of the ab initio based potential energy surfaces.

Signatures of non-adiabatic dynamics in the fine-structure state distributions of the OH(X̃/Ã) products in the B-band photodissociation of H2O.

PubMed

Zhou, Linsen; Xie, Daiqian; Guo, Hua

2015-03-28

A detailed quantum mechanical characterization of the photodissociation dynamics of H2O at 121.6 nm is presented. The calculations were performed using a full-dimensional wave packet method on coupled potential energy surfaces of all relevant electronic states. Our state-to-state model permits a detailed analysis of the OH(X̃/Ã) product fine-structure populations as a probe of the non-adiabatic dissociation dynamics. The calculated rotational state distributions of the two Λ-doublet levels of OH(X̃, v = 0) exhibit very different characteristics. The A' states, produced mostly via the B̃→X̃ conical intersection pathway, have significantly higher populations than the A″ counterparts, which are primarily from the B̃→Ã Renner-Teller pathway. The former features a highly inverted and oscillatory rotational state distribution, while the latter has a smooth distribution with much less rotational excitation. In good agreement with experiment, the calculated total OH(X̃) rotational state distribution and anisotropy parameters show clear even-odd oscillations, which can be attributed to a quantum mechanical interference between waves emanating from the HOH and HHO conical intersections in the B̃→X̃ non-adiabatic pathway. On the other hand, the experiment-theory agreement for the OH(Ã) fragment is also satisfactory, although some small quantitative differences suggest remaining imperfections of the ab initio based potential energy surfaces.

Ligand induced change of β2 adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis.

PubMed

Bai, Qifeng; Pérez-Sánchez, Horacio; Zhang, Yang; Shao, Yonghua; Shi, Danfeng; Liu, Huanxiang; Yao, Xiaojun

2014-08-14

The reported crystal structures of β2 adrenergic receptor (β2AR) reveal that the open and closed states of the water channel are correlated with the inactive and active conformations of β2AR. However, more details about the process by which the water channel states are affected by the active to inactive conformational change of β2AR remain illusive. In this work, molecular dynamics simulations are performed to study the dynamical inactive and active conformational change of β2AR induced by inverse agonist ICI 118,551. Markov state model analysis and free energy calculation are employed to explore the open and close states of the water channel. The simulation results show that inverse agonist ICI 118,551 can induce water channel opening during the conformational transition of β2AR. Markov state model (MSM) analysis proves that the energy contour can be divided into seven states. States S1, S2 and S5, which represent the active conformation of β2AR, show that the water channel is in the closed state, while states S4 and S6, which correspond to the intermediate state conformation of β2AR, indicate the water channel opens gradually. State S7, which represents the inactive structure of β2AR, corresponds to the full open state of the water channel. The opening mechanism of the water channel is involved in the ligand-induced conformational change of β2AR. These results can provide useful information for understanding the opening mechanism of the water channel and will be useful for the rational design of potent inverse agonists of β2AR.

Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states and should be identified to obtain a full view of the transitions. Therefore, we developed an enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways. In the DPDS method, molecular dynamics simulations are carried out on the targeting PES within a chain-of-states framework to directly sample the transition pathway space. The simulations of DPDS could be regulated by two parameters controlling distance among states along the pathway and smoothness of the pathway. One advantage of the chain-of-states framework is that no specific reaction coordinates are necessary to generate the reaction pathway, because such information is implicitly represented by the structures along the pathway. The chain-of-states setup in a DPDS method greatly enhances the sufficient sampling in high-energy space between two end states, such as transition states. By removing the constraint on the end states of the pathway, DPDS will also sample pathways connecting minima on a PES in addition to the end points of the starting pathway. This feature makes DPDS an ideal method to directly explore transition pathway space. Three examples demonstrate the efficiency of DPDS methods in sampling the high-energy area important for reactions on the PES.

Hairpin exact coherent states in channel flow

NASA Astrophysics Data System (ADS)

Graham, Michael; Shekar, Ashwin

2017-11-01

Questions remain over the role of hairpin vortices in fully developed turbulent flows. Studies have shown that hairpins play a role in the dynamics away from the wall but the question still persists if they play any part in (near wall) fully developed turbulent dynamics. In addition, the robustness of the hairpin vortex regeneration mechanism is still under investigation. Recent studies have shown the existence of nonlinear traveling wave solutions to the Navier-Stokes equations, also known as exact coherent states (ECS), that capture many aspects of near-wall turbulent structures. Previously discovered ECS in channel flow have a quasi-streamwise vortex structure, with no indication of hairpin formation. Here we present a family of traveling wave solutions for channel flow that displays hairpin vortices. They have a streamwise vortex-streak structure near the wall with a spatially localized hairpin head near the channel centerline, attached to and sustained by the near wall structures. This family of solutions emerges through a transcritical bifurcation from a branch of traveling wave solutions with y and z reflectional symmetry. We also look into the instabilities that lead to the development of hairpins also explore its connection to turbulent dynamics.

Femtosecond x-ray scattering study of ultrafast photoinduced structural dynamics in solvated [ Co ( terpy ) 2 ] 2 +

DOE PAGES

Biasin, Elisa; van Driel, Tim Brandt; Kjær, Kasper S.; ...

2016-06-30

Here, we study the structural dynamics of photoexcited [Co(terpy) 2] 2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitation event leads to elongation of the Co-N bonds, followed by coherent Co-N bond length oscillations arising from the impulsive excitation of a vibrational mode dominated by the symmetrical stretch of all six Co-N bonds. This mode has a period of 0.33 ps and decays on a subpicosecond time scale. We find that the equilibrium bond-elongated structure of themore » high spin state is established on a single-picosecond time scale and that this state has a lifetime of ~7 ps.« less

Protein flexibility in the light of structural alphabets

PubMed Central

Craveur, Pierrick; Joseph, Agnel P.; Esque, Jeremy; Narwani, Tarun J.; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S.; Bhaskara, Ramachandra M.; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G.

2015-01-01

Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. PMID:26075209

Application of dynamic recurrent neural networks in nonlinear system identification

NASA Astrophysics Data System (ADS)

Du, Yun; Wu, Xueli; Sun, Huiqin; Zhang, Suying; Tian, Qiang

2006-11-01

An adaptive identification method of simple dynamic recurrent neural network (SRNN) for nonlinear dynamic systems is presented in this paper. This method based on the theory that by using the inner-states feed-back of dynamic network to describe the nonlinear kinetic characteristics of system can reflect the dynamic characteristics more directly, deduces the recursive prediction error (RPE) learning algorithm of SRNN, and improves the algorithm by studying topological structure on recursion layer without the weight values. The simulation results indicate that this kind of neural network can be used in real-time control, due to its less weight values, simpler learning algorithm, higher identification speed, and higher precision of model. It solves the problems of intricate in training algorithm and slow rate in convergence caused by the complicate topological structure in usual dynamic recurrent neural network.

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.

PubMed

Ahnert, S E; Fink, T M A

2016-07-01

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. © 2016 The Authors.

Meiotic recombination modulates the structure and dynamics of the synaptonemal complex during C. elegans meiosis

PubMed Central

2017-01-01

During meiotic prophase, a structure called the synaptonemal complex (SC) assembles at the interface between aligned pairs of homologous chromosomes, and crossover recombination events occur between their DNA molecules. Here we investigate the inter-relationships between these two hallmark features of the meiotic program in the nematode C. elegans, revealing dynamic properties of the SC that are modulated by recombination. We demonstrate that the SC incorporates new subunits and switches from a more highly dynamic/labile state to a more stable state as germ cells progress through the pachytene stage of meiotic prophase. We further show that the more dynamic state of the SC is prolonged in mutants where meiotic recombination is impaired. Moreover, in meiotic mutants where recombination intermediates are present in limiting numbers, SC central region subunits become preferentially stabilized on the subset of chromosome pairs that harbor a site where pro-crossover factors COSA-1 and MutSγ are concentrated. Polo-like kinase PLK-2 becomes preferentially localized to the SCs of chromosome pairs harboring recombination sites prior to the enrichment of SC central region proteins on such chromosomes, and PLK-2 is required for this enrichment to occur. Further, late pachytene nuclei in a plk-2 mutant exhibit the more highly dynamic SC state. Together our data demonstrate that crossover recombination events elicit chromosome-autonomous stabilizing effects on the SC and implicate PLK-2 in this process. We discuss how this recombination-triggered modulation of SC state might contribute to regulatory mechanisms that operate during meiosis to ensure the formation of crossovers while at the same time limiting their numbers. PMID:28339470

Water dynamics in glass ionomer cements

NASA Astrophysics Data System (ADS)

Berg, M. C.; Jacobsen, J.; Momsen, N. C. R.; Benetti, A. R.; Telling, M. T. F.; Seydel, T.; Bordallo, H. N.

2016-07-01

Glass ionomer cements (GIC) are an alternative for preventive dentistry. However, these dental cements are complex systems where important motions related to the different states of the hydrogen atoms evolve in a confined porous structure. In this paper, we studied the water dynamics of two different liquids used to prepare either conventional or resin-modified glass ionomer cement. By combining thermal analysis with neutron scattering data we were able to relate the water structure in the liquids to the materials properties.

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states

PubMed Central

Linnemann, Amelia K.; Krawetz, Stephen A.

2010-01-01

Summary The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease. PMID:20948980

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states.

PubMed

Linnemann, Amelia K; Krawetz, Stephen A

2009-01-01

The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease.

UV absorption spectrum and photodissociation channels of the simplest Criegee intermediate (CH2OO).

PubMed

Dawes, Richard; Jiang, Bin; Guo, Hua

2015-01-14

The lowest-lying singlet states of the simplest Criegee intermediate (CH2OO) have been characterized along the O-O dissociation coordinate using explicitly correlated MRCI-F12 electronic structure theory and large active spaces. It is found that a high-level treatment of dynamic electron-correlation is essential to accurately describe these states. A significant well on the B-state is identified at the MRCI-F12 level with an equilibrium structure that differs substantially from that of the ground X-state. This well is presumably responsible for the apparent vibrational structure in some experimental UV absorption spectra, analogous to the structured Huggins band of the iso-electronic ozone. The B-state potential in the Franck-Condon region is sufficiently accurate that an absorption spectrum calculated with a one-dimensional model agrees remarkably well with experiment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use inmore » combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.« less

Ontology of Earth's nonlinear dynamic complex systems

NASA Astrophysics Data System (ADS)

Babaie, Hassan; Davarpanah, Armita

2017-04-01

As a complex system, Earth and its major integrated and dynamically interacting subsystems (e.g., hydrosphere, atmosphere) display nonlinear behavior in response to internal and external influences. The Earth Nonlinear Dynamic Complex Systems (ENDCS) ontology formally represents the semantics of the knowledge about the nonlinear system element (agent) behavior, function, and structure, inter-agent and agent-environment feedback loops, and the emergent collective properties of the whole complex system as the result of interaction of the agents with other agents and their environment. It also models nonlinear concepts such as aperiodic, random chaotic behavior, sensitivity to initial conditions, bifurcation of dynamic processes, levels of organization, self-organization, aggregated and isolated functionality, and emergence of collective complex behavior at the system level. By incorporating several existing ontologies, the ENDCS ontology represents the dynamic system variables and the rules of transformation of their state, emergent state, and other features of complex systems such as the trajectories in state (phase) space (attractor and strange attractor), basins of attractions, basin divide (separatrix), fractal dimension, and system's interface to its environment. The ontology also defines different object properties that change the system behavior, function, and structure and trigger instability. ENDCS will help to integrate the data and knowledge related to the five complex subsystems of Earth by annotating common data types, unifying the semantics of shared terminology, and facilitating interoperability among different fields of Earth science.

Shape dependent electronic structure and exciton dynamics in small In(Ga)As quantum dots

NASA Astrophysics Data System (ADS)

Gomis, J.; Martínez-Pastor, J.; Alén, B.; Granados, D.; García, J. M.; Roussignol, P.

2006-12-01

We present a study of the primary optical transitions and recombination dynamics in InGaAs self-assembled quantum nanostructures with different shape. Starting from the same quantum dot seeding layer, and depending on the overgrowth conditions, these new nanostructures can be tailored in shape and are characterized by heights lower than 2 nm and base lengths around 100 nm. The geometrical shape strongly influences the electronic and optical properties of these nanostructuctures. We measure for them ground state optical transitions in the range 1.25 1.35 eV and varying energy splitting between their excited states. The temperature dependence of the exciton recombination dynamics is reported focusing on the intermediate temperature regime (before thermal escape begins to be important). In this range, an important increase of the effective photoluminescence decay time is observed and attributed to the state filling and exciton thermalization between excited and ground states. A rate equation model is also developed reproducing quite well the observed exciton dynamics.

Structure of the low-lying positive parity states in the proton-neutron symplectic model

NASA Astrophysics Data System (ADS)

Ganev, H. G.

2018-05-01

The proton-neutron symplectic model with Sp(12, R) dynamical symmetry is applied for the simultaneous description of the microscopic structure of the low-lying states of the ground state, γ and β bands in 166 Er. For this purpose, the model Hamiltonian is diagonalized in the space of stretched states by exploiting the SUp (3) ⊗ SUn (3) symmetry-adapted basis. The theoretical predictions are compared with experiment and some other microscopic collective models, like the one-component Sp(6, R) symplectic and pseudo-SU(3) models. A good description of the energy levels of the three bands under consideration, as well as the enhanced intraband B(E2) transition strengths between the states of the ground and γ bands is obtained without the use of effective charges. The results show the presence of a good SU(3) dynamical symmetry. It is also shown that, in contrast to the Sp(6, R) case, the lowest excited bands, e.g., the β and γ bands, naturally appear together with the ground state band within a single Sp(12, R) irreducible representation.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

PubMed

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.

PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

PubMed

Heo, Lim; Feig, Michael

2018-03-15

Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. feig@msu.edu. Supplementary data are available at Bioinformatics online.

Exploring the underlying structure of mental disorders: cross-diagnostic differences and similarities from a network perspective using both a top-down and a bottom-up approach.

PubMed

Wigman, J T W; van Os, J; Borsboom, D; Wardenaar, K J; Epskamp, S; Klippel, A; Viechtbauer, W; Myin-Germeys, I; Wichers, M

2015-08-01

It has been suggested that the structure of psychopathology is best described as a complex network of components that interact in dynamic ways. The goal of the present paper was to examine the concept of psychopathology from a network perspective, combining complementary top-down and bottom-up approaches using momentary assessment techniques. A pooled Experience Sampling Method (ESM) dataset of three groups (individuals with a diagnosis of depression, psychotic disorder or no diagnosis) was used (pooled N = 599). The top-down approach explored the network structure of mental states across different diagnostic categories. For this purpose, networks of five momentary mental states ('cheerful', 'content', 'down', 'insecure' and 'suspicious') were compared between the three groups. The complementary bottom-up approach used principal component analysis to explore whether empirically derived network structures yield meaningful higher order clusters. Individuals with a clinical diagnosis had more strongly connected moment-to-moment network structures, especially the depressed group. This group also showed more interconnections specifically between positive and negative mental states than the psychotic group. In the bottom-up approach, all possible connections between mental states were clustered into seven main components that together captured the main characteristics of the network dynamics. Our combination of (i) comparing network structure of mental states across three diagnostically different groups and (ii) searching for trans-diagnostic network components across all pooled individuals showed that these two approaches yield different, complementary perspectives in the field of psychopathology. The network paradigm therefore may be useful to map transdiagnostic processes.

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

PubMed

Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

2017-01-01

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation

PubMed Central

Zhao, Liling; Cao, Zanxia; Wang, Jihua

2012-01-01

To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain. PMID:22408419

Dynamical states, possibilities and propagation of stress signal

PubMed Central

Malik, Md. Zubbair; Ali, Shahnawaz; Singh, Soibam Shyamchand; Ishrat, Romana; Singh, R. K. Brojen

2017-01-01

The stress driven dynamics of Notch-Wnt-p53 cross-talk is subjected to a few possible dynamical states governed by simple fractal rules, and allowed to decide its own fate by choosing one of these states which are contributed from long range correlation with varied fluctuations due to active molecular interaction. The topological properties of the networks corresponding to these dynamical states have hierarchical features with assortive structure. The stress signal driven by nutlin and modulated by mediator GSK3 acts as anti-apoptotic signal in this system, whereas, the stress signal driven by Axin and modulated by GSK3 behaves as anti-apoptotic for a certain range of Axin and GSK3 interaction, and beyond which the signal acts as favor-apoptotic signal. However, this stress system prefers to stay in an active dynamical state whose counterpart complex network is closest to hierarchical topology with exhibited roles of few interacting hubs. During the propagation of stress signal, the system allows the propagator pathway to inherit all possible properties of the state to the receiver pathway/pathways with slight modifications, indicating efficient information processing and democratic sharing of responsibilities in the system via cross-talk. The increase in the number of cross-talk pathways in the system favors to establish self-organization. PMID:28106087

Dynamical states, possibilities and propagation of stress signal.

PubMed

Malik, Md Zubbair; Ali, Shahnawaz; Singh, Soibam Shyamchand; Ishrat, Romana; Singh, R K Brojen

2017-01-20

The stress driven dynamics of Notch-Wnt-p53 cross-talk is subjected to a few possible dynamical states governed by simple fractal rules, and allowed to decide its own fate by choosing one of these states which are contributed from long range correlation with varied fluctuations due to active molecular interaction. The topological properties of the networks corresponding to these dynamical states have hierarchical features with assortive structure. The stress signal driven by nutlin and modulated by mediator GSK3 acts as anti-apoptotic signal in this system, whereas, the stress signal driven by Axin and modulated by GSK3 behaves as anti-apoptotic for a certain range of Axin and GSK3 interaction, and beyond which the signal acts as favor-apoptotic signal. However, this stress system prefers to stay in an active dynamical state whose counterpart complex network is closest to hierarchical topology with exhibited roles of few interacting hubs. During the propagation of stress signal, the system allows the propagator pathway to inherit all possible properties of the state to the receiver pathway/pathways with slight modifications, indicating efficient information processing and democratic sharing of responsibilities in the system via cross-talk. The increase in the number of cross-talk pathways in the system favors to establish self-organization.

Cooperation dynamics of generalized reciprocity in state-based social dilemmas

NASA Astrophysics Data System (ADS)

Stojkoski, Viktor; Utkovski, Zoran; Basnarkov, Lasko; Kocarev, Ljupco

2018-05-01

We introduce a framework for studying social dilemmas in networked societies where individuals follow a simple state-based behavioral mechanism based on generalized reciprocity, which is rooted in the principle "help anyone if helped by someone." Within this general framework, which applies to a wide range of social dilemmas including, among others, public goods, donation, and snowdrift games, we study the cooperation dynamics on a variety of complex network examples. By interpreting the studied model through the lenses of nonlinear dynamical systems, we show that cooperation through generalized reciprocity always emerges as the unique attractor in which the overall level of cooperation is maximized, while simultaneously exploitation of the participating individuals is prevented. The analysis elucidates the role of the network structure, here captured by a local centrality measure which uniquely quantifies the propensity of the network structure to cooperation by dictating the degree of cooperation displayed both at the microscopic and macroscopic level. We demonstrate the applicability of the analysis on a practical example by considering an interaction structure that couples a donation process with a public goods game.

Dynamic Structure Factor and Transport Coefficients of a Homogeneously Driven Granular Fluid in Steady State

NASA Astrophysics Data System (ADS)

Vollmayr-Lee, Katharina; Zippelius, Annette; Aspelmeier, Timo

2011-03-01

We study the dynamic structure factor of a granular fluid of hard spheres, driven into a stationary nonequilibrium state by balancing the energy loss due to inelastic collisions with the energy input due to driving. The driving is chosen to conserve momentum, so that fluctuating hydrodynamics predicts the existence of sound modes. We present results of computer simulations which are based on an event driven algorithm. The dynamic structure factor F (q , ω) is determined for volume fractions 0.05, 0.1 and 0.2 and coefficients of normal restitution 0.8 and 0.9. We observe sound waves, and compare our results for F (q , ω) with the predictions of generalized fluctuating hydrodynamics which takes into account that temperature fluctuations decay either diffusively or with a finite relaxation rate, depending on wave number and inelasticity. We determine the speed of sound and the transport coefficients and compare them to the results of kinetic theory. K.V.L. thanks the Institute of Theoretical Physics, University of Goettingen, for financial support and hospitality.

Molecular dynamics studies of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Ding, Feng

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.

Breaking Symmetry in Time-Dependent Electronic Structure Theory to Describe Spectroscopic Properties of Non-Collinear and Chiral Molecules

NASA Astrophysics Data System (ADS)

Goings, Joshua James

Time-dependent electronic structure theory has the power to predict and probe the ways electron dynamics leads to useful phenomena and spectroscopic data. Here we report several advances and extensions of broken-symmetry time-dependent electronic structure theory in order to capture the flexibility required to describe non-equilibrium spin dynamics, as well as electron dynamics for chiroptical properties and vibrational effects. In the first half, we begin by discussing the generalization of self-consistent field methods to the so-called two-component structure in order to capture non-collinear spin states. This means that individual electrons are allowed to take a superposition of spin-1/2 projection states, instead of being constrained to either spin-up or spin-down. The system is no longer a spin eigenfunction, and is known a a spin-symmetry broken wave function. This flexibility to break spin symmetry may lead to variational instabilities in the approximate wave function, and we discuss how these may be overcome. With a stable non-collinear wave function in hand, we then discuss how to obtain electronic excited states from the non-collinear reference, along with associated challenges in their physical interpretation. Finally, we extend the two-component methods to relativistic Hamiltonians, which is the proper setting for describing spin-orbit driven phenomena. We describe the first implementation of the explicit time propagation of relativistic two-component methods and how this may be used to capture spin-forbidden states in electronic absorption spectra. In the second half, we describe the extension of explicitly time-propagated wave functions to the simulation of chiroptical properties, namely circular dichroism (CD) spectra of chiral molecules. Natural circular dichroism, that is, CD in the absence of magnetic fields, originates in the broken parity symmetry of chiral molecules. This proves to be an efficient method for computing circular dichroism spectra for high density-of-states chiral molecules. Next, we explore the impact of allowing nuclear motion on electronic absorption spectra within the context of mixed quantum-classical dynamics. We show that nuclear motion modulates the electronic response, and this gives rise to infrared absorption as well as Raman scattering phenomena in the computed dynamic polarizability. Finally, we explore the accuracy of several perturbative approximations to the equation-of-motion coupled-cluster methods for the efficient and accurate prediction of electronic absorption spectra.

Troponin structure: its modulation by Ca(2+) and phosphorylation studied by molecular dynamics simulations.

PubMed

Zamora, Juan Eiros; Papadaki, Maria; Messer, Andrew E; Marston, Steven B; Gould, Ian R

2016-07-27

The only available crystal structure of the human cardiac troponin molecule (cTn) in the Ca(2+) activated state does not include crucial segments, including the N-terminus of the cTn inhibitory subunit (cTnI). We have applied all-atom molecular dynamics (MD) simulations to study the structure and dynamics of cTn, both in the unphosphorylated and bis-phosphorylated states at Ser23/Ser24 of cTnI. We performed multiple microsecond MD simulations of wild type (WT) cTn (6, 5 μs) and bisphosphorylated (SP23/SP24) cTn (9 μs) on a 419 amino acid cTn model containing human sequence cTnC (1-161), cTnI (1-171) and cTnT (212-298), including residues not present in the crystal structure. We have compared our results to previous computational studies, and proven that longer simulations and a water box of at least 25 Å are needed to sample the interesting conformational shifts both in the native and bis-phosphorylated states. As a consequence of the introduction into the model of the C-terminus of cTnT that was missing in previous studies, cTnC-cTnI interactions that are responsible for the cTn dynamics are altered. We have also shown that phosphorylation does not increase cTn fluctuations, and its effects on the protein-protein interaction profiles cannot be assessed in a significant way. Finally, we propose that phosphorylation could provoke a loss of Ca(2+) by stabilizing out-of-coordination distances of the cTnC's EF hand II residues, and in particular Ser 69.

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein.

PubMed

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E; Fernandez-Alberti, Sebastian

2015-06-28

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

NASA Astrophysics Data System (ADS)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E.; Fernandez-Alberti, Sebastian

2015-06-01

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

Atomic-scale structural signature of dynamic heterogeneities in metallic liquids

NASA Astrophysics Data System (ADS)

Pasturel, Alain; Jakse, Noel

2017-08-01

With sufficiently high cooling rates, liquids will cross their equilibrium melting temperatures and can be maintained in a metastable undercooled state before solidifying. Studies of undercooled liquids reveal several intriguing dynamic phenomena and because explicit connections between liquid structure and liquids dynamics are difficult to identify, it remains a major challenge to capture the underlying structural link to these phenomena. Ab initio molecular dynamics (AIMD) simulations are yet especially powerful in providing atomic-scale details otherwise not accessible in experiments. Through the AIMD-based study of Cr additions in Al-based liquids, we evidence for the first time a close relationship between the decoupling of component diffusion and the emergence of dynamic heterogeneities in the undercooling regime. In addition, we demonstrate that the origin of both phenomena is related to a structural heterogeneity caused by a strong interplay between chemical short-range order (CSRO) and local fivefold topology (ISRO) at the short-range scale in the liquid phase that develops into an icosahedral-based medium-range order (IMRO) upon undercooling. Finally, our findings reveal that this structural signature is also captured in the temperature dependence of partial pair-distribution functions which opens up the route to more elaborated experimental studies.

Finite element dynamic analysis of soft tissues using state-space model.

PubMed

Iorga, Lucian N; Shan, Baoxiang; Pelegri, Assimina A

2009-04-01

A finite element (FE) model is employed to investigate the dynamic response of soft tissues under external excitations, particularly corresponding to the case of harmonic motion imaging. A solid 3D mixed 'u-p' element S8P0 is implemented to capture the near-incompressibility inherent in soft tissues. Two important aspects in structural modelling of these tissues are studied; these are the influence of viscous damping on the dynamic response and, following FE-modelling, a developed state-space formulation that valuates the efficiency of several order reduction methods. It is illustrated that the order of the mathematical model can be significantly reduced, while preserving the accuracy of the observed system dynamics. Thus, the reduced-order state-space representation of soft tissues for general dynamic analysis significantly reduces the computational cost and provides a unitary framework for the 'forward' simulation and 'inverse' estimation of soft tissues. Moreover, the results suggest that damping in soft-tissue is significant, effectively cancelling the contribution of all but the first few vibration modes.

Asymmetry in band widening and quasiparticle lifetimes in SrVO3: Competition between screened exchange and local correlations from combined G W and dynamical mean-field theory G W + DMFT

NASA Astrophysics Data System (ADS)

Tomczak, Jan M.; Casula, M.; Miyake, T.; Biermann, S.

2014-10-01

The very first dynamical implementation of the combined GW and dynamical mean-field scheme "G W + DMFT " for a real material was achieved recently [Tomczak et al., Europhys. Lett. 100, 67001 (2012), 10.1209/0295-5075/100/67001], and applied to the ternary transition metal oxide SrVO3. Here, we review and extend that work, giving not only a detailed account of full G W + DMFT calculations, but also discussing and testing simplified approximate schemes. We give insights into the nature of exchange and correlation effects: dynamical renormalizations in the Fermi liquid regime of SrVO3 are essentially local, and nonlocal correlations mainly act to screen the Fock exchange term. The latter substantially widens the quasiparticle band structure, while the band narrowing induced by the former is accompanied by a spectral weight transfer to higher energies. Most interestingly, the exchange broadening is more pronounced in the unoccupied part of the spectrum than in the occupied one. In addition, shorter lifetimes for unoccupied states further contribute to making the corrections to the Kohn-Sham band structure asymmetric with respect to the chemical potential. As a result, the G W + DMFT electronic structure of SrVO3 resembles the conventional density functional based dynamical mean-field (DFT + DMFT ) description for occupied states but is profoundly modified in the empty part. Our work leads to a reinterpretation of inverse photoemission spectroscopy (IPES) data. Indeed, we assign a prominent peak at about 2.7 eV dominantly to eg states, rather than to an upper Hubbard band of t2 g character. Similar surprises can be expected for other transition metal oxides. This prediction urgently calls for more detailed investigations of conduction band states in correlated materials.

Excited state conformational dynamics in carotenoids: dark intermediates and excitation energy transfer.

PubMed

Beck, Warren F; Bishop, Michael M; Roscioli, Jerome D; Ghosh, Soumen; Frank, Harry A

2015-04-15

A consideration of the excited state potential energy surfaces of carotenoids develops a new hypothesis for the nature of the conformational motions that follow optical preparation of the S2 (1(1)Bu(+)) state. After an initial displacement from the Franck-Condon geometry along bond length alternation coordinates, it is suggested that carotenoids pass over a transition-state barrier leading to twisted conformations. This hypothesis leads to assignments for several dark intermediate states encountered in femtosecond spectroscopic studies. The Sx state is assigned to the structure reached upon the onset of torsional motions near the transition state barrier that divides planar and twisted structures on the S2 state potential energy surface. The X state, detected recently in two-dimensional electronic spectra, corresponds to a twisted structure well past the barrier and approaching the S2 state torsional minimum. Lastly, the S(∗) state is assigned to a low lying S1 state structure with intramolecular charge transfer character (ICT) and a pyramidal conformation. It follows that the bent and twisted structures of carotenoids that are found in photosynthetic light-harvesting proteins yield excited-state structures that favor the development of an ICT character and optimized energy transfer yields to (bacterio)chlorophyll acceptors. Copyright © 2015 Elsevier Inc. All rights reserved.

Impedance measures in analysis and characterization of multistable structures subjected to harmonic excitation

NASA Astrophysics Data System (ADS)

Harne, Ryan L.; Goodpaster, Benjamin A.

2018-01-01

Structural components susceptible to adverse, post-buckled dynamic behaviors have long challenged the success of applications requiring lightweight, slender curved structures, while researchers have begun to leverage such bistable systems in emerging applications for novel energy attenuation and shape-changing properties. To expedite development and deployment of these built-up platforms containing post-buckled constituents, efficient approaches are required to complement time-consuming full-field models in the prediction of the near- and far-from-equilibrium dynamics. This research meets the need by introducing a semi-analytical model framework to enable the characterization of steady-state responses in multi degree-of-freedom (DOF) and multistable structural systems subjected to harmonic excitation. In so doing, the pathway for assessing impedance measures is created here so as to identify how energy travels and returns within built-up multistable structures. Verified by simulations and qualitatively validated by experiments, the analysis is shown to accurately reproduce both near- and far-from-equilibrium responses including different classes of energetic snap-through dynamics that only exist in such multistable structures. A first look at the impedance measures of different dynamic regimes reveals a connection between damping in multistable structures and the sustainability of far-from-equilibrium oscillations.

Electronic structure and relaxation dynamics in a superconducting topological material

DOE PAGES

Neupane, Madhab; Ishida, Yukiaki; Sankar, Raman; ...

2016-03-03

Topological superconductors host new states of quantum matter which show a pairing gap in the bulk and gapless surface states providing a platform to realize Majorana fermions. Recently, alkaline-earth metal Sr intercalated Bi2Se3 has been reported to show superconductivity with a Tc~3K and a large shielding fraction. Here we report systematic normal state electronic structure studies of Sr0.06Bi2Se3 (Tc~2.5K) by performing photoemission spectroscopy. Using angle-resolved photoemission spectroscopy (ARPES), we observe a quantum well confined two-dimensional (2D) state coexisting with a topological surface state in Sr0.06Bi2Se3. Furthermore, our time-resolved ARPES reveals the relaxation dynamics showing different decay mechanism between the excitedmore » topological surface states and the two-dimensional states. Our experimental observation is understood by considering the intra-band scattering for topological surface states and an additional electron phonon scattering for the 2D states, which is responsible for the superconductivity. Our first-principles calculations agree with the more effective scattering and a shorter lifetime of the 2D states. In conclusion, our results will be helpful in understanding low temperature superconducting states of these topological materials.« less

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites.

PubMed

Wise, John G

2012-06-26

Multidrug resistance proteins that belong to the ATP-binding cassette family like the human P-glycoprotein (ABCB1 or Pgp) are responsible for many failed cancer and antiviral chemotherapies because these membrane transporters remove the chemotherapeutics from the targeted cells. Understanding the details of the catalytic mechanism of Pgp is therefore critical to the development of inhibitors that might overcome these resistances. In this work, targeted molecular dynamics techniques were used to elucidate catalytically relevant structures of Pgp. Crystal structures of homologues in four different conformations were used as intermediate targets in the dynamics simulations. Transitions from conformations that were wide open to the cytoplasm to transition state conformations that were wide open to the extracellular space were studied. Twenty-six nonredundant transitional protein structures were identified from these targeted molecular dynamics simulations using evolutionary structure analyses. Coupled movement of nucleotide binding domains (NBDs) and transmembrane domains (TMDs) that form the drug binding cavities were observed. Pronounced twisting of the NBDs as they approached each other as well as the quantification of a dramatic opening of the TMDs to the extracellular space as the ATP hydrolysis transition state was reached were observed. Docking interactions of 21 known transport ligands or inhibitors were analyzed with each of the 26 transitional structures. Many of the docking results obtained here were validated by previously published biochemical determinations. As the ATP hydrolysis transition state was approached, drug docking in the extracellular half of the transmembrane domains seemed to be destabilized as transport ligand exit gates opened to the extracellular space.

Ultrafast electronic dynamics in unipolar n-doped indium gallium arsenide/gallium arsenide self-assembled quantum dots

NASA Astrophysics Data System (ADS)

Wu, Zong-Kwei J.

2006-12-01

Photodetectors based on intraband infrared absorption in the quantum dots have demonstrated improved performance over its quantum well counterpart by lower dark current, relative temperature insensitivity, and its ability for normal incidence operation. Various scattering processes, including phonon emission/absorption and carrier-carrier scattering, are critical in understanding device operation on the fundamental level. In previous studies, our group has investigated carrier dynamics in both low- and high-density regime. Ultrafast electron-hole scattering and the predicted phonon bottleneck effect in intrinsic quantum dots have been observed. Further examination on electron dynamics in unipolar structures is presented in this thesis. We used n-doped quantum dot in mid-infrared photodetector device structure to study the electron dynamics in unipolar structure. Differential transmission spectroscopy with mid-infrared intraband pump and optical interband probe was implemented to measure the electron dynamics directly without creating extra electron-hole pair, Electron relaxation after excitation was measured under various density and temperature conditions. Rapid capture into quantum dot within ˜ 10 ps was observed due to Auger-type electron-electron scattering. Intradot relaxation from the quantum dot excited state to the ground state was also observed on the time scale of 100 ps. With highly doped electron density in the structure, the inter-sublevel relaxation is dominated by Auger-type electron-electron scattering and the phonon bottleneck effect is circumvented. Nanosecond-scale recovery in larger-sized quantum dots was observed, not intrinsic to electron dynamics but due to band-bending and built-in voltage drift. An ensemble Monte Carlo simulation was also established to model the dynamics in quantum dots and in goad agreement with the experimental results. We presented a comprehensive picture of electron dynamics in the unipolar quantum dot structure. Although the phonon bottleneck is circumvented with high doped electron density, relaxation processes in unipolar quantum dots have been measured with time scales longer than that of bipolar systems. The results explain the operation principles of the quantum dot infrared photodetector on a microscopic level and provide basic understanding for future applications and designs.

Excited state dynamics of thiophene and bithiophene: new insights into theoretically challenging systems.

PubMed

Prlj, Antonio; Curchod, Basile F E; Corminboeuf, Clémence

2015-06-14

The computational elucidation and proper description of the ultrafast deactivation mechanisms of simple organic electronic units, such as thiophene and its oligomers, is as challenging as it is contentious. A comprehensive excited state dynamics analysis of these systems utilizing reliable electronic structure approaches is currently lacking, with earlier pictures of the photochemistry of these systems being conceived based upon high-level static computations or lower level dynamic trajectories. Here a detailed surface hopping molecular dynamics of thiophene and bithiophene using the algebraic diagrammatic construction to second order (ADC(2)) method is presented. Our findings illustrate that ring puckering plays an important role in thiophene photochemistry and that the photostability increases when going upon dimerization into bithiophene.

Quantum theory of phonon-mediated decoherence and relaxation of two-level systems in a structured electromagnetic reservoir

NASA Astrophysics Data System (ADS)

Roy, Chiranjeeb

In this thesis we study the role of nonradiative degrees of freedom on quantum optical properties of mesoscopic quantum dots placed in the structured electromagnetic reservoir of a photonic crystal. We derive a quantum theory of the role of acoustic and optical phonons in modifying the optical absorption lineshape, polarization dynamics, and population dynamics of a two-level atom (quantum dot) in the "colored" electromagnetic vacuum of a photonic band gap (PBG) material. This is based on a microscopic Hamiltonian describing both radiative and vibrational processes quantum mechanically. Phonon sidebands in an ordinary electromagnetic reservoir are recaptured in a simple model of optical phonons using a mean-field factorization of the atomic and lattice displacement operators. Our formalism is then used to treat the non-Markovian dynamics of the same system within the structured electromagnetic density of states of a photonic crystal. We elucidate the extent to which phonon-assisted decay limits the lifetime of a single photon-atom bound state and derive the modified spontaneous emission dynamics due to coupling to various phonon baths. We demonstrate that coherent interaction with undamped phonons can lead to enhanced lifetime of a photon-atom bound state in a PBG by (i) dephasing and reducing the transition electric dipole moment of the atom and (ii) reducing the quantum mechanical overlap of the state vectors of the excited and ground state (polaronic shift). This results in reduction of the steady-state atomic polarization but an increase in the fractionalized upper state population in the photon-atom bound state. We demonstrate, on the other hand, that the lifetime of the photon-atom bound state in a PBG is limited by the lifetime of phonons due to lattice anharmonicities (break-up of phonons into lower energy phonons) and purely nonradiative decay. We demonstrate how these additional damping effects limit the extent of the polaronic (Franck-Condon) shift of the atomic excited state. We also derive the modified polarization decay and dephasing rates in the presence of such damping. This leads to a microscopic, quantum theory of the optical absorption lineshapes. Our model and formalism provide a starting point for describing dephasing and relaxation in the presence of external coherent fields and multiple quantum dot interactions in electromagnetic reservoirs with radiative memory effects.

Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-10-01

The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.

Optimal regeneration planning for old-growth forest: addressing scientific uncertainty in endangered species recovery through adaptive management

USGS Publications Warehouse

Moore, C.T.; Conroy, M.J.

2006-01-01

Stochastic and structural uncertainties about forest dynamics present challenges in the management of ephemeral habitat conditions for endangered forest species. Maintaining critical foraging and breeding habitat for the endangered red-cockaded woodpecker (Picoides borealis) requires an uninterrupted supply of old-growth forest. We constructed and optimized a dynamic forest growth model for the Piedmont National Wildlife Refuge (Georgia, USA) with the objective of perpetuating a maximum stream of old-growth forest habitat. Our model accommodates stochastic disturbances and hardwood succession rates, and uncertainty about model structure. We produced a regeneration policy that was indexed by current forest state and by current weight of evidence among alternative model forms. We used adaptive stochastic dynamic programming, which anticipates that model probabilities, as well as forest states, may change through time, with consequent evolution of the optimal decision for any given forest state. In light of considerable uncertainty about forest dynamics, we analyzed a set of competing models incorporating extreme, but plausible, parameter values. Under any of these models, forest silviculture practices currently recommended for the creation of woodpecker habitat are suboptimal. We endorse fully adaptive approaches to the management of endangered species habitats in which predictive modeling, monitoring, and assessment are tightly linked.

A mathematical analysis of the effects of Hebbian learning rules on the dynamics and structure of discrete-time random recurrent neural networks.

PubMed

Siri, Benoît; Berry, Hugues; Cessac, Bruno; Delord, Bruno; Quoy, Mathias

2008-12-01

We present a mathematical analysis of the effects of Hebbian learning in random recurrent neural networks, with a generic Hebbian learning rule, including passive forgetting and different timescales, for neuronal activity and learning dynamics. Previous numerical work has reported that Hebbian learning drives the system from chaos to a steady state through a sequence of bifurcations. Here, we interpret these results mathematically and show that these effects, involving a complex coupling between neuronal dynamics and synaptic graph structure, can be analyzed using Jacobian matrices, which introduce both a structural and a dynamical point of view on neural network evolution. Furthermore, we show that sensitivity to a learned pattern is maximal when the largest Lyapunov exponent is close to 0. We discuss how neural networks may take advantage of this regime of high functional interest.

Thermodynamics of RNA structures by Wang–Landau sampling

PubMed Central

Lou, Feng; Clote, Peter

2010-01-01

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures. Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations. Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/. Contact: clote@bc.edu PMID:20529917

Thermomechanical Response of Shape Memory Alloy Hybrid Composites. Degree awarded by Virginia Polytechnic Inst. and State Univ., Blackburg, Virginia, Nov. 2000.

NASA Technical Reports Server (NTRS)

Turner, Travis L.

2001-01-01

This study examines the use of embedded shape memory alloy (SMA) actuators for adaptive control of the thermomechanical response of composite structures. A nonlinear thermomechanical model is presented for analyzing shape memory alloy hybrid composite (SMAHC) structures exposed to steady-state thermal and dynamic mechanical loads. Also presented are (1) fabrication procedures for SMAHC specimens, (2) characterization of the constituent materials for model quantification, (3) development of the test apparatus for conducting static and dynamic experiments on specimens with and without SMA, (4) discussion of the experimental results, and (5) validation of the analytical and numerical tools developed in the study. Excellent agreement is achieved between the predicted and measured SAMHC responses including thermal buckling, thermal post-buckling and dynamic response due to inertial loading. The validated model and thermomechanical analysis tools are used to demonstrate a variety of static and dynamic response behaviors including control of static (thermal buckling and post-buckling) and dynamic responses (vibration, sonic fatigue, and acoustic transmission). and SMAHC design considerations for these applications. SMAHCs are shown to have significant advantages over conventional response abatement approaches for vibration, sonic fatigue, and noise control.

Structural model for fluctuations in financial markets

NASA Astrophysics Data System (ADS)

Anand, Kartik; Khedair, Jonathan; Kühn, Reimer

2018-05-01

In this paper we provide a comprehensive analysis of a structural model for the dynamics of prices of assets traded in a market which takes the form of an interacting generalization of the geometric Brownian motion model. It is formally equivalent to a model describing the stochastic dynamics of a system of analog neurons, which is expected to exhibit glassy properties and thus many metastable states in a large portion of its parameter space. We perform a generating functional analysis, introducing a slow driving of the dynamics to mimic the effect of slowly varying macroeconomic conditions. Distributions of asset returns over various time separations are evaluated analytically and are found to be fat-tailed in a manner broadly in line with empirical observations. Our model also allows us to identify collective, interaction-mediated properties of pricing distributions and it predicts pricing distributions which are significantly broader than their noninteracting counterparts, if interactions between prices in the model contain a ferromagnetic bias. Using simulations, we are able to substantiate one of the main hypotheses underlying the original modeling, viz., that the phenomenon of volatility clustering can be rationalized in terms of an interplay between the dynamics within metastable states and the dynamics of occasional transitions between them.

Optimal estimation of recurrence structures from time series

NASA Astrophysics Data System (ADS)

beim Graben, Peter; Sellers, Kristin K.; Fröhlich, Flavio; Hutt, Axel

2016-05-01

Recurrent temporal dynamics is a phenomenon observed frequently in high-dimensional complex systems and its detection is a challenging task. Recurrence quantification analysis utilizing recurrence plots may extract such dynamics, however it still encounters an unsolved pertinent problem: the optimal selection of distance thresholds for estimating the recurrence structure of dynamical systems. The present work proposes a stochastic Markov model for the recurrent dynamics that allows for the analytical derivation of a criterion for the optimal distance threshold. The goodness of fit is assessed by a utility function which assumes a local maximum for that threshold reflecting the optimal estimate of the system's recurrence structure. We validate our approach by means of the nonlinear Lorenz system and its linearized stochastic surrogates. The final application to neurophysiological time series obtained from anesthetized animals illustrates the method and reveals novel dynamic features of the underlying system. We propose the number of optimal recurrence domains as a statistic for classifying an animals' state of consciousness.

Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

DOE PAGES

van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; ...

2016-11-28

The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir 2(dimen) 4] 2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling themore » solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.« less

Dynamics of the GB3 loop regions from MD simulation: how much of it is real?

PubMed

Li, Tong; Jing, Qingqing; Yao, Lishan

2011-04-07

A total of 1.1 μs of molecular dynamics (MD) simulations were performed to study the structure and dynamics of protein GB3. The simulation motional amplitude of the loop regions is generally overestimated in comparison with the experimental backbone N-H order parameters S(2). Two-state behavior is observed for several residues in these regions, with the minor state population in the range of 3-13%. Further inspection suggests that the (φ, ψ) dihedral angles of the minor states deviate from the GB3 experimental values, implying the existence of nonnative states. After fitting the MD trajectories of these residues to the NMR RDCs, the minor state populations are significantly reduced by at least 80%, suggesting that MD simulations are strongly biased toward the minor states, thus overestimating the dynamics of the loop regions. The optimized trajectories produce intra, sequential H(N)-H(α) RDCs and intra (3)J(HNHα) that are not included in the trajectories fitting for these residues that are closer to the experimental data. Unlike GB3, 0.55 μs MD simulations of protein ubiquitin do not show distinctive minor states, and the derived NMR order parameters are better converged. Our findings indicate that the artifacts of the simulations depend on the specific system studied and that one should be cautious interpreting the enhanced dihedral dynamics from long MD simulations.

Near-infrared light-responsive dynamic wrinkle patterns.

PubMed

Li, Fudong; Hou, Honghao; Yin, Jie; Jiang, Xuesong

2018-04-01

Dynamic micro/nanopatterns provide an effective approach for on-demand tuning of surface properties to realize a smart surface. We report a simple yet versatile strategy for the fabrication of near-infrared (NIR) light-responsive dynamic wrinkles by using a carbon nanotube (CNT)-containing poly(dimethylsiloxane) (PDMS) elastomer as the substrate for the bilayer systems, with various functional polymers serving as the top stiff layers. The high photon-to-thermal energy conversion of CNT leads to the NIR-controlled thermal expansion of the elastic CNT-PDMS substrate, resulting in dynamic regulation of the applied strain (ε) of the bilayer system by the NIR on/off cycle to obtain a reversible wrinkle pattern. The switchable surface topological structures can transfer between the wrinkled state and the wrinkle-free state within tens of seconds via NIR irradiation. As a proof-of-concept application, this type of NIR-driven dynamic wrinkle pattern was used in smart displays, dynamic gratings, and light control electronics.

Integral projection models for finite populations in a stochastic environment.

PubMed

Vindenes, Yngvild; Engen, Steinar; Saether, Bernt-Erik

2011-05-01

Continuous types of population structure occur when continuous variables such as body size or habitat quality affect the vital parameters of individuals. These structures can give rise to complex population dynamics and interact with environmental conditions. Here we present a model for continuously structured populations with finite size, including both demographic and environmental stochasticity in the dynamics. Using recent methods developed for discrete age-structured models we derive the demographic and environmental variance of the population growth as functions of a continuous state variable. These two parameters, together with the expected population growth rate, are used to define a one-dimensional diffusion approximation of the population dynamics. Thus, a substantial reduction in complexity is achieved as the dynamics of the complex structured model can be described by only three population parameters. We provide methods for numerical calculation of the model parameters and demonstrate the accuracy of the diffusion approximation by computer simulation of specific examples. The general modeling framework makes it possible to analyze and predict future dynamics and extinction risk of populations with various types of structure, and to explore consequences of changes in demography caused by, e.g., climate change or different management decisions. Our results are especially relevant for small populations that are often of conservation concern.

Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

PubMed

Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

2016-04-14

Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties.

Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

PubMed Central

Warfield, Becka M.

2017-01-01

RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are present the population of binding-competent aptamer states increases more than twofold. This population change, rather than direct interactions between Mg2+ and theophylline, accounts for altered theophylline binding kinetics. PMID:28437473

Indicators of ecosystem function identify alternate states in the sagebrush steppe.

PubMed

Kachergis, Emily; Rocca, Monique E; Fernandez-Gimenez, Maria E

2011-10-01

Models of ecosystem change that incorporate nonlinear dynamics and thresholds, such as state-and-transition models (STMs), are increasingly popular tools for land management decision-making. However, few models are based on systematic collection and documentation of ecological data, and of these, most rely solely on structural indicators (species composition) to identify states and transitions. As STMs are adopted as an assessment framework throughout the United States, finding effective and efficient ways to create data-driven models that integrate ecosystem function and structure is vital. This study aims to (1) evaluate the utility of functional indicators (indicators of rangeland health, IRH) as proxies for more difficult ecosystem function measurements and (2) create a data-driven STM for the sagebrush steppe of Colorado, USA, that incorporates both ecosystem structure and function. We sampled soils, plant communities, and IRH at 41 plots with similar clayey soils but different site histories to identify potential states and infer the effects of management practices and disturbances on transitions. We found that many IRH were correlated with quantitative measures of functional indicators, suggesting that the IRH can be used to approximate ecosystem function. In addition to a reference state that functions as expected for this soil type, we identified four biotically and functionally distinct potential states, consistent with the theoretical concept of alternate states. Three potential states were related to management practices (chemical and mechanical shrub treatments and seeding history) while one was related only to ecosystem processes (erosion). IRH and potential states were also related to environmental variation (slope, soil texture), suggesting that there are environmental factors within areas with similar soils that affect ecosystem dynamics and should be noted within STMs. Our approach generated an objective, data-driven model of ecosystem dynamics for rangeland management. Our findings suggest that the IRH approximate ecosystem processes and can distinguish between alternate states and communities and identify transitions when building data-driven STMs. Functional indicators are a simple, efficient way to create data-driven models that are consistent with alternate state theory. Managers can use them to improve current model-building methods and thus apply state-and-transition models more broadly for land management decision-making.

Modeling Temporal Behavior in Large Networks: A Dynamic Mixed-Membership Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossi, R; Gallagher, B; Neville, J

Given a large time-evolving network, how can we model and characterize the temporal behaviors of individual nodes (and network states)? How can we model the behavioral transition patterns of nodes? We propose a temporal behavior model that captures the 'roles' of nodes in the graph and how they evolve over time. The proposed dynamic behavioral mixed-membership model (DBMM) is scalable, fully automatic (no user-defined parameters), non-parametric/data-driven (no specific functional form or parameterization), interpretable (identifies explainable patterns), and flexible (applicable to dynamic and streaming networks). Moreover, the interpretable behavioral roles are generalizable, computationally efficient, and natively supports attributes. We applied ourmore » model for (a) identifying patterns and trends of nodes and network states based on the temporal behavior, (b) predicting future structural changes, and (c) detecting unusual temporal behavior transitions. We use eight large real-world datasets from different time-evolving settings (dynamic and streaming). In particular, we model the evolving mixed-memberships and the corresponding behavioral transitions of Twitter, Facebook, IP-Traces, Email (University), Internet AS, Enron, Reality, and IMDB. The experiments demonstrate the scalability, flexibility, and effectiveness of our model for identifying interesting patterns, detecting unusual structural transitions, and predicting the future structural changes of the network and individual nodes.« less

Reinforcement learning algorithms for robotic navigation in dynamic environments.

PubMed

Yen, Gary G; Hickey, Travis W

2004-04-01

The purpose of this study was to examine improvements to reinforcement learning (RL) algorithms in order to successfully interact within dynamic environments. The scope of the research was that of RL algorithms as applied to robotic navigation. Proposed improvements include: addition of a forgetting mechanism, use of feature based state inputs, and hierarchical structuring of an RL agent. Simulations were performed to evaluate the individual merits and flaws of each proposal, to compare proposed methods to prior established methods, and to compare proposed methods to theoretically optimal solutions. Incorporation of a forgetting mechanism did considerably improve the learning times of RL agents in a dynamic environment. However, direct implementation of a feature-based RL agent did not result in any performance enhancements, as pure feature-based navigation results in a lack of positional awareness, and the inability of the agent to determine the location of the goal state. Inclusion of a hierarchical structure in an RL agent resulted in significantly improved performance, specifically when one layer of the hierarchy included a feature-based agent for obstacle avoidance, and a standard RL agent for global navigation. In summary, the inclusion of a forgetting mechanism, and the use of a hierarchically structured RL agent offer substantially increased performance when compared to traditional RL agents navigating in a dynamic environment.

Functional connectivity dynamically evolves on multiple time-scales over a static structural connectome: Models and mechanisms.

PubMed

Cabral, Joana; Kringelbach, Morten L; Deco, Gustavo

2017-10-15

Over the last decade, we have observed a revolution in brain structural and functional Connectomics. On one hand, we have an ever-more detailed characterization of the brain's white matter structural connectome. On the other, we have a repertoire of consistent functional networks that form and dissipate over time during rest. Despite the evident spatial similarities between structural and functional connectivity, understanding how different time-evolving functional networks spontaneously emerge from a single structural network requires analyzing the problem from the perspective of complex network dynamics and dynamical system's theory. In that direction, bottom-up computational models are useful tools to test theoretical scenarios and depict the mechanisms at the genesis of resting-state activity. Here, we provide an overview of the different mechanistic scenarios proposed over the last decade via computational models. Importantly, we highlight the need of incorporating additional model constraints considering the properties observed at finer temporal scales with MEG and the dynamical properties of FC in order to refresh the list of candidate scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

NASA Astrophysics Data System (ADS)

Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

2017-01-01

Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

Coarse-Grained Lattice Model Simulations of Sequence-Structure Fitness of a Ribosome-Inactivating Protein

DTIC Science & Technology

2007-11-05

limits of what is considered practical when applying all-atom molecular - dynamics simulation methods. Lattice models provide computationally robust...of expectation values from the density of states. All-atom molecular - dynamics simulations provide the most rigorous sampling method to generate con... molecular - dynamics simulations of protein folding,6–9 reported studies of computing a heat capacity or other calorimetric observables have been limited to

Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

2018-01-01

We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

Edge mixing dynamics in graphene p–n junctions in the quantum Hall regime

PubMed Central

Matsuo, Sadashige; Takeshita, Shunpei; Tanaka, Takahiro; Nakaharai, Shu; Tsukagoshi, Kazuhito; Moriyama, Takahiro; Ono, Teruo; Kobayashi, Kensuke

2015-01-01

Massless Dirac electron systems such as graphene exhibit a distinct half-integer quantum Hall effect, and in the bipolar transport regime co-propagating edge states along the p–n junction are realized. Additionally, these edge states are uniformly mixed at the junction, which makes it a unique structure to partition electrons in these edge states. Although many experimental works have addressed this issue, the microscopic dynamics of electron partition in this peculiar structure remains unclear. Here we performed shot-noise measurements on the junction in the quantum Hall regime as well as at zero magnetic field. We found that, in sharp contrast with the zero-field case, the shot noise in the quantum Hall regime is finite in the bipolar regime, but is strongly suppressed in the unipolar regime. Our observation is consistent with the theoretical prediction and gives microscopic evidence that the edge states are uniquely mixed along the p–n junction. PMID:26337445

Exploration of the Energy Landscape of Acetylcholinesterase by Molecular Dynamics Simulation.

NASA Astrophysics Data System (ADS)

McCammon, J. Andrew

2002-03-01

Proteins have rough energy landscapes. Often more states than just the ground state are occupied and have biological functions. It is essential to study these conformational substates and the dynamical transitions among them. Acetylcholinesterase (AChE) is an important enzyme that has biological functions including the termination of synaptic transmission signals. X-ray structures show that it has an active site that is accessible only via a long and narrow channel from its surface. Therefore the fact that acetylcholine and larger ligands can reach the active site is believed to reflect the protein's structural fluctuation. We carried out long molecular dynamics simulations to investigate the dynamics of AChE and its relation to biological function, and compared our results with experiments. The results reveal several "doors" that open intermittantly between the active site and the surface. Instead of having simple exponential decay correlation functions, the time series of these channels reveal complex, fractal gating between conformations. We also compared the AChE dynamics data with those from an AchE-fasciculin complex. (Fasciculin is a small protein that is a natural inhibitor of AChE.) The results show remarkable effects of the protein-protein interaction, including allosteric and dynamical inhibition by fasciculin besides direct steric blocking. More information and images can be found at http://mccammon.ucsd.edu

Femtosecond dynamics of a non-steroidal anti-inflammatory drug (piroxicam) in solution: The involvement of twisting motion

NASA Astrophysics Data System (ADS)

Gil, Michał; Douhal, Abderrazzak

2008-06-01

In this contribution, we report on fast and ultrafast dynamics of a non-steroidal anti-inflammatory drug, piroxicam (PX), in methyl acetate (MAC) and triacetin (TAC), two solvents of different viscosities. The enol form of PX undergoes a femtosecond (shorter than 100 fs) electronically excited state intramolecular proton-transfer reaction to produce keto tautomers. These structures exhibit an internal twisting motion to generate keto rotamers in ˜2-5 ps, a time being longer in TAC. The transient absorption/emission spectrum is very broad indicating that the potential-energy surface at the electronically excited state is very flat, and reflecting the involvement of several coordinates along which the wavepacket of the fs-produced structures evolve.

REVIEWS OF TOPICAL PROBLEMS: Nonlinear dynamics of the brain: emotion and cognition

NASA Astrophysics Data System (ADS)

Rabinovich, Mikhail I.; Muezzinoglu, M. K.

2010-07-01

Experimental investigations of neural system functioning and brain activity are standardly based on the assumption that perceptions, emotions, and cognitive functions can be understood by analyzing steady-state neural processes and static tomographic snapshots. The new approaches discussed in this review are based on the analysis of transient processes and metastable states. Transient dynamics is characterized by two basic properties, structural stability and information sensitivity. The ideas and methods that we discuss provide an explanation for the occurrence of and successive transitions between metastable states observed in experiments, and offer new approaches to behavior analysis. Models of the emotional and cognitive functions of the brain are suggested. The mathematical object that represents the observed transient brain processes in the phase space of the model is a structurally stable heteroclinic channel. The possibility of using the suggested models to construct a quantitative theory of some emotional and cognitive functions is illustrated.

Using simulation to interpret experimental data in terms of protein conformational ensembles.

PubMed

Allison, Jane R

2017-04-01

In their biological environment, proteins are dynamic molecules, necessitating an ensemble structural description. Molecular dynamics simulations and solution-state experiments provide complimentary information in the form of atomically detailed coordinates and averaged or distributions of structural properties or related quantities. Recently, increases in the temporal and spatial scale of conformational sampling and comparison of the more diverse conformational ensembles thus generated have revealed the importance of sampling rare events. Excitingly, new methods based on maximum entropy and Bayesian inference are promising to provide a statistically sound mechanism for combining experimental data with molecular dynamics simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Implications of tristability in pattern-forming ecosystems

NASA Astrophysics Data System (ADS)

Zelnik, Yuval R.; Gandhi, Punit; Knobloch, Edgar; Meron, Ehud

2018-03-01

Many ecosystems show both self-organized spatial patterns and multistability of possible states. The combination of these two phenomena in different forms has a significant impact on the behavior of ecosystems in changing environments. One notable case is connected to tristability of two distinct uniform states together with patterned states, which has recently been found in model studies of dryland ecosystems. Using a simple model, we determine the extent of tristability in parameter space, explore its effects on the system dynamics, and consider its implications for state transitions or regime shifts. We analyze the bifurcation structure of model solutions that describe uniform states, periodic patterns, and hybrid states between the former two. We map out the parameter space where these states exist, and note how the different states interact with each other. We further focus on two special implications with ecological significance, breakdown of the snaking range and complex fronts. We find that the organization of the hybrid states within a homoclinic snaking structure breaks down as it meets a Maxwell point where simple fronts are stationary. We also discover a new series of complex fronts between the uniform states, each with its own velocity. We conclude with a brief discussion of the significance of these findings for the dynamics of regime shifts and their potential control.

Theoretical study of the potential energy surfaces and dynamics of CaNC/CaCN

NASA Astrophysics Data System (ADS)

Nanbu, Shinkoh; Minamino, Satoshi; Aoyagi, Mutsumi

1997-05-01

Potential energy surfaces for the ground and two low-lying electronically excited states of CaNC/CaCN, are calculated using the ab initio molecular orbital (MO) configuration interaction (CI) method. The absorption and emission spectra of the system are computed by performing time-dependent quantum dynamical calculations on these surfaces. The most stable geometries for the two lowest lying 12Σ+ and 12Π electronic states correspond to the calcium isocyanide (CaNC) structure. These two states are characterized by ionic bonding and the potential energy curves along the bending coordinate are relatively isotropic. The result of our wave packet dynamics shows that the characteristics of the experimental spectra observed by the laser-induced fluorescence spectroscopy can be explained by the Renner-Teller splitting.

Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malaby, Andrew W.; Das, Sanchaita; Chakravarthy, Srinivas

Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization andmore » conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.« less

The combination of circle topology and leaky integrator neurons remarkably improves the performance of echo state network on time series prediction.

PubMed

Xue, Fangzheng; Li, Qian; Li, Xiumin

2017-01-01

Recently, echo state network (ESN) has attracted a great deal of attention due to its high accuracy and efficient learning performance. Compared with the traditional random structure and classical sigmoid units, simple circle topology and leaky integrator neurons have more advantages on reservoir computing of ESN. In this paper, we propose a new model of ESN with both circle reservoir structure and leaky integrator units. By comparing the prediction capability on Mackey-Glass chaotic time series of four ESN models: classical ESN, circle ESN, traditional leaky integrator ESN, circle leaky integrator ESN, we find that our circle leaky integrator ESN shows significantly better performance than other ESNs with roughly 2 orders of magnitude reduction of the predictive error. Moreover, this model has stronger ability to approximate nonlinear dynamics and resist noise than conventional ESN and ESN with only simple circle structure or leaky integrator neurons. Our results show that the combination of circle topology and leaky integrator neurons can remarkably increase dynamical diversity and meanwhile decrease the correlation of reservoir states, which contribute to the significant improvement of computational performance of Echo state network on time series prediction.

Importance of strong-correlation on the lattice dynamics of light-actinides Th-Pa alloy

NASA Astrophysics Data System (ADS)

de La Peã+/-A Seaman, Omar; Heid, Rolf; Bohnen, Klaus-Peter

We have studied the structural, electronic, and lattice dynamics of the Th1-xPax actinide alloy. This system have been analyzed within the framework of density functional perturbation theory, using a mixed-basis pseudopotential method and the virtual crystal approximation (VCA) for modeling the alloy. In particular, the energetics is analyzed as the ground-state crystal structure is changed form fcc to bct, as well as the electronic density of states (DOS), and the phonon frequencies. Such properties have been calculated with and without strong correlations effects through the LDA+U formalism. Although the strong-correlation does not influence on a great manner the Th properties, such effects are more important as the content increases towards Pa, affecting even the definition of the ground-state crystal structure for Pa (experimentally determined as bct). The evolution of the density of states at the Fermi level (N (EF)) and the phonon frequencies as a function of Pa-content are presented and discussed in detail, aiming to understand their influence on the electron-phonon coupling for the Th-Pa alloy. This research was supported by Conacyt-México under project No. CB2013-221807-F.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

PubMed

Parton, Daniel L; Grinaway, Patrick B; Hanson, Sonya M; Beauchamp, Kyle A; Chodera, John D

2016-06-01

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs)-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.

Method of performing computational aeroelastic analyses

NASA Technical Reports Server (NTRS)

Silva, Walter A. (Inventor)

2011-01-01

Computational aeroelastic analyses typically use a mathematical model for the structural modes of a flexible structure and a nonlinear aerodynamic model that can generate a plurality of unsteady aerodynamic responses based on the structural modes for conditions defining an aerodynamic condition of the flexible structure. In the present invention, a linear state-space model is generated using a single execution of the nonlinear aerodynamic model for all of the structural modes where a family of orthogonal functions is used as the inputs. Then, static and dynamic aeroelastic solutions are generated using computational interaction between the mathematical model and the linear state-space model for a plurality of periodic points in time.

Magnetic structure and excitation spectrum of the hyperhoneycomb Kitaev magnet β -Li2IrO3

NASA Astrophysics Data System (ADS)

Ducatman, Samuel; Rousochatzakis, Ioannis; Perkins, Natalia B.

2018-03-01

We present a theoretical study of the static and dynamical properties of the three-dimensional, hyperhoneycomb Kitaev magnet β -Li2IrO3 . We argue that the observed incommensurate order can be understood in terms of a long-wavelength twisting of a nearby commensurate period-3 state, with the same key qualitatively features. The period-3 state shows very different structure when either the Kitaev interaction K or the off-diagonal exchange anisotropy Γ is dominant. A comparison of the associated static spin structure factors with reported scattering experiments in zero and finite fields gives strong evidence that β -Li2IrO3 lies in the regime of dominant Kitaev coupling, and that the Heisenberg exchange J is much weaker than both K and Γ . Our predictions for the magnon excitation spectra, the dynamical spin structure factors, and their polarization dependence provide additional distinctive fingerprints that can be checked experimentally.

Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α.

PubMed

Delaforge, Elise; Milles, Sigrid; Bouvignies, Guillaume; Bouvier, Denis; Boivin, Stephane; Salvi, Nicola; Maurin, Damien; Martel, Anne; Round, Adam; Lemke, Edward A; Jensen, Malene Ringkjøbing; Hart, Darren J; Blackledge, Martin

2015-12-09

Influenza A RNA polymerase complex is formed from three components, PA, PB1, and PB2. PB2 is independently imported into the nucleus prior to polymerase reconstitution. All crystallographic structures of the PB2 C-terminus (residues 536-759) reveal two globular domains, 627 and NLS, that form a tightly packed heterodimer. The molecular basis of the affinity of 627-NLS for importins remained unclear from these structures, apparently requiring large-scale conformational changes prior to importin binding. Using a combination of solution-state NMR, small-angle neutron scattering, small-angle X-ray scattering (SAXS), and Förster resonance energy transfer (FRET), we show that 627-NLS populates a temperature-dependent dynamic equilibrium between closed and open states. The closed state is stabilized by a tripartite salt bridge involving the 627-NLS interface and the linker, that becomes flexible in the open state, with 627 and NLS dislocating into a highly dynamic ensemble. Activation enthalpies and entropies associated with the rupture of this interface were derived from simultaneous analysis of temperature-dependent chemical exchange saturation transfer measurements, revealing a strong temperature dependence of both open-state population and exchange rate. Single-molecule FRET and SAXS demonstrate that only the open-form is capable of binding to importin α and that, upon binding, the 627 domain samples a dynamic conformational equilibrium in the vicinity of the C-terminus of importin α. This intrinsic large-scale conformational flexibility therefore enables 627-NLS to bind importin through conformational selection from a temperature-dependent equilibrium comprising both functional forms of the protein.

Growth and yield of white spruce plantations in the Lake States (a literature review).

Treesearch

H. Michael Rauscher

1984-01-01

This summary of the white spruce literature covers the structure, site relations, population dynamics, and cultural practices applicable to established plantations in the Lake States. The objective of this paper is to assemble and organize all information relevant to the silviculture, growth, and yield of white spruce plantations in the Lake States .

Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

NASA Astrophysics Data System (ADS)

Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

2016-05-01

The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

Folding and stability of helical bundle proteins from coarse-grained models.

PubMed

Kapoor, Abhijeet; Travesset, Alex

2013-07-01

We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Copyright © 2013 Wiley Periodicals, Inc.

Self-organization of cosmic radiation pressure instability

NASA Technical Reports Server (NTRS)

Hogan, Craig J.

1991-01-01

Under some circumstances the absorption of radiation momentum by an absorbing medium opens the possibility of a dynamical instability, sometimes called 'mock gravity'. Here, a simplified abstract model is studied in which the radiation source is assumed to remain spatially uniform, there is no reabsorption or reradiated light, and no forces other than radiative pressure act on the absorbing medium. It is shown that this model displays the unique feature of being not only unstable, but also self-organizing. The structure approaches a statistical dynamical steady state which is almost independent of initial conditions. In this saturated state the absorbers are concentrated in thin walls around empty bubbles; as the instability develops the big bubbles get bigger and the small ones get crushed and disappear. A linear analysis shows that to first order the thin walls are indeed stable structures. It is speculated that this instability may play a role in forming cosmic large-scale structure.

The role of symmetry in the regulation of brain dynamics

NASA Astrophysics Data System (ADS)

Tang, Evelyn; Giusti, Chad; Cieslak, Matthew; Grafton, Scott; Bassett, Danielle

Synchronous neural processes regulate a wide range of behaviors from attention to learning. Yet structural constraints on these processes are far from understood. We draw on new theoretical links between structural symmetries and the control of synchronous function, to offer a reconceptualization of the relationships between brain structure and function in human and non-human primates. By classifying 3-node motifs in macaque connectivity data, we find the most prevalent motifs can theoretically ensure a diversity of function including strict synchrony as well as control to arbitrary states. The least prevalent motifs are theoretically controllable to arbitrary states, which may not be desirable in a biological system. In humans, regions with high topological similarity of connections (a continuous notion related to symmetry) are most commonly found in fronto-parietal systems, which may account for their critical role in cognitive control. Collectively, our work underscores the role of symmetry and topological similarity in regulating dynamics of brain function.

Structural signal of a dynamic glass transition

NASA Astrophysics Data System (ADS)

Chattopadhyay, Sudeshna; Uysal, Ahmet; Stripe, Benjamin; Evmenenko, Guennadi; Dutta, Pulak; Ehrlich, Steven; Karapetrova, Evguenia A.

2010-03-01

Conventional wisdom states that there is no significant difference between the static structures of the glass and liquid states of a given material. Using x-ray reflectivity, we have studied pentaphenyl trimethyl trisiloxane, an isotropic liquid at room temperature with a dynamic glass transition at 224K. Surface density oscillations (surface layers) develop below 285K, similar to those seen in other metallic and dielectric liquids and in computer simulations [1]. Upon cooling further, there is a sharp increase in the penetration of the surface layers into the bulk material, i.e. an apparently discontinuous change in the static structure, exactly at the glass transition (224K) [2]. [4pt] [1]. e.g. O. M. Magnussen et al., PRL 74, 4444 (1995); H. Mo et al. PRL 96, 096107 (2006); E. Chac'on et al., PRL 87, 166101 (2001) [0pt] [2] S. Chattopadhyay et al, PRL 103, 175701 (2009)

Excitons in Single-Walled Carbon Nanotubes and Their Dynamics

NASA Astrophysics Data System (ADS)

Amori, Amanda R.; Hou, Zhentao; Krauss, Todd D.

2018-04-01

Understanding exciton dynamics in single-walled carbon nanotubes (SWCNTs) is essential to unlocking the many potential applications of these materials. This review summarizes recent progress in understanding exciton photophysics and, in particular, exciton dynamics in SWCNTs. We outline the basic physical and electronic properties of SWCNTs, as well as bright and dark transitions within the framework of a strongly bound one-dimensional excitonic model. We discuss the many facets of ultrafast carrier dynamics in SWCNTs, including both single-exciton states (bright and dark) and multiple-exciton states. Photophysical properties that directly relate to excitons and their dynamics, including exciton diffusion lengths, chemical and structural defects, environmental effects, and photoluminescence photon statistics as observed through photon antibunching measurements, are also discussed. Finally, we identify a few key areas for advancing further research in the field of SWCNT excitons and photonics.

Mode localization in the cooperative dynamics of protein recognition

NASA Astrophysics Data System (ADS)

Copperman, J.; Guenza, M. G.

2016-07-01

The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. This paper presents a study on the correlation between local fluctuations, binding, and biological function for two sample proteins, starting from the Langevin Equation for Protein Dynamics (LE4PD). The LE4PD is a microscopic and residue-specific coarse-grained approach to protein dynamics, which starts from the static structural ensemble of a protein and predicts the dynamics analytically. It has been shown to be accurate in its prediction of NMR relaxation experiments and Debye-Waller factors. The LE4PD is solved in a set of diffusive modes which span a vast range of time scales of the protein dynamics, and provides a detailed picture of the mode-dependent localization of the fluctuation as a function of the primary structure of the protein. To investigate the dynamics of protein complexes, the theory is implemented here to treat the coarse-grained dynamics of interacting macromolecules. As an example, calculations of the dynamics of monomeric and dimerized HIV protease and the free Insulin Growth Factor II Receptor (IGF2R) domain 11 and its IGF2R:IGF2 complex are presented. Either simulation-derived or experimentally measured NMR conformers are used as input structural ensembles to the theory. The picture that emerges suggests a dynamical heterogeneous protein where biologically active regions provide energetically comparable conformational states that are trapped by a reacting partner in agreement with the conformation-selection mechanism of binding.

Timescales of Coherent Dynamics in the Light Harvesting Complex 2 (LH2) of Rhodobacter sphaeroides.

PubMed

Fidler, Andrew F; Singh, Ved P; Long, Phillip D; Dahlberg, Peter D; Engel, Gregory S

2013-05-02

The initial dynamics of energy transfer in the light harvesting complex 2 from Rhodobacter sphaeroides were investigated with polarization controlled two-dimensional spectroscopy. This method allows only the coherent electronic motions to be observed revealing the timescale of dephasing among the excited states. We observe persistent coherence among all states and assign ensemble dephasing rates for the various coherences. A simple model is utilized to connect the spectroscopic transitions to the molecular structure, allowing us to distinguish coherences between the two rings of chromophores and coherences within the rings. We also compare dephasing rates between excited states to dephasing rates between the ground and excited states, revealing that the coherences between excited states dephase on a slower timescale than coherences between the ground and excited states.

The short-lived signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes.

PubMed

Ramachandran, Pradeep L; Lovett, Janet E; Carl, Patrick J; Cammarata, Marco; Lee, Jae Hyuk; Jung, Yang Ouk; Ihee, Hyotcherl; Timmel, Christiane R; van Thor, Jasper J

2011-06-22

The signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump-probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 Å upon illumination. The SAXS/WAXS difference signal for the signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from (1)H-(15)N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump-probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the I(2)' state (also referred to as the 'pB' state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I(2)' state, which is structurally modeled by dynamical annealing and refinement calculations.

The Molecular Dynamics Study of the Structural Conversions in the Transformer Protein RfaH

NASA Astrophysics Data System (ADS)

Gc, Jeevan; Gerstman, Bernard; Chapagain, Prem

Recently, a class of multi-domain proteins such as RfaH transcription factor are labelled as the transformer proteins as they undergo major conformational transformation for performing multiple functions. In the absence of the inter-domain contacts, the C-terminal domain of RfaH transforms from its alpha-helix conformation to a beta-barrel structure. Each of these states have their own functional role: in its alpha-helx state, RfaH-CTD inhibits the transcription by masking the binding site of RNAP, but in its beta state it facilitates the translation. We used various molecular dynamics simulations to study its transformer-like behavior of full-RfaH and identified key amino acid residues that are important in modulating such behavior. Our results show that the inter domain interactions constitute the major barrier in the alpha-helix to beta-barrel conversion. Once the interfacial interactions are broken, structural conversion is easier. The structural conversion from beta-barrel to alpha-helix proceeds with the rearrangement of the hydrophobic residues followed by the inter domain contacts formation via non-native, transient salt-bridge formation, leading to the formation of the native inter domain salt-bridge and hydrophobic contacts to give the final alpha-helix structure.

Femtosecond Heterodyne Transient Grating Detection of Conformational Dynamics in the S0 (11Ag-) State of Carotenoids After Nonradiative Decay of the S2 (11Bu+) State

NASA Astrophysics Data System (ADS)

Roscioli, Jerome D.; Ghosh, Soumen; Bishop, Michael M.; Lafountain, Amy M.; Frank, Harry A.; Beck, Warren F.

Transient grating spectroscopy was used to study the dynamics of nonradiative decay of the S1 (21Ag-) state in ß-carotene and peridinin after optical preparation of the S2) state. The kinetics of the recovery of the absorption and dispersion components of the third-order signal exhibit significantly different time constants. For β-carotene in benzonitrile, the absorption and dispersion recovery time constants are 11.6 and 10.2 ps. For peridinin in methanol, the time constants are 9.9 and 7.4 ps. These results indicate that the initial product of the decay of the S1 state is a conformationally displaced structure. The decay rate for the S1 state and the conformational relaxation rate are both slowed in peridinin as the polarity of the solvent decreases; in ethyl acetate, the conformational relaxation time constant is 45 ps, which rules out a dominant contribution from vibrational cooling. These results indicate that the S1 state develops intramolecular charge transfer character owing to distortions along torsional and out-of-plane coordinates, with a pyramidal structure favored as the most stable conformation. Recovery of the photoselected ground state conformation involves a reverse charge-transfer event followed by relaxation to a planar structure. Work supported by Photosynthetic Systems Program of the U.S. Department of Energy under Grant DE-SC0010847.

Flight Dynamics of Flexible Aircraft with Aeroelastic and Inertial Force Interactions

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Tuzcu, Ilhan

2009-01-01

This paper presents an integrated flight dynamic modeling method for flexible aircraft that captures coupled physics effects due to inertial forces, aeroelasticity, and propulsive forces that are normally present in flight. The present approach formulates the coupled flight dynamics using a structural dynamic modeling method that describes the elasticity of a flexible, twisted, swept wing using an equivalent beam-rod model. The structural dynamic model allows for three types of wing elastic motion: flapwise bending, chordwise bending, and torsion. Inertial force coupling with the wing elasticity is formulated to account for aircraft acceleration. The structural deflections create an effective aeroelastic angle of attack that affects the rigid-body motion of flexible aircraft. The aeroelastic effect contributes to aerodynamic damping forces that can influence aerodynamic stability. For wing-mounted engines, wing flexibility can cause the propulsive forces and moments to couple with the wing elastic motion. The integrated flight dynamics for a flexible aircraft are formulated by including generalized coordinate variables associated with the aeroelastic-propulsive forces and moments in the standard state-space form for six degree-of-freedom flight dynamics. A computational structural model for a generic transport aircraft has been created. The eigenvalue analysis is performed to compute aeroelastic frequencies and aerodynamic damping. The results will be used to construct an integrated flight dynamic model of a flexible generic transport aircraft.

Sensor selection cost optimisation for tracking structurally cyclic systems: a P-order solution

NASA Astrophysics Data System (ADS)

Doostmohammadian, M.; Zarrabi, H.; Rabiee, H. R.

2017-08-01

Measurements and sensing implementations impose certain cost in sensor networks. The sensor selection cost optimisation is the problem of minimising the sensing cost of monitoring a physical (or cyber-physical) system. Consider a given set of sensors tracking states of a dynamical system for estimation purposes. For each sensor assume different costs to measure different (realisable) states. The idea is to assign sensors to measure states such that the global cost is minimised. The number and selection of sensor measurements need to ensure the observability to track the dynamic state of the system with bounded estimation error. The main question we address is how to select the state measurements to minimise the cost while satisfying the observability conditions. Relaxing the observability condition for structurally cyclic systems, the main contribution is to propose a graph theoretic approach to solve the problem in polynomial time. Note that polynomial time algorithms are suitable for large-scale systems as their running time is upper-bounded by a polynomial expression in the size of input for the algorithm. We frame the problem as a linear sum assignment with solution complexity of ?.

Functional connectivity dynamics: modeling the switching behavior of the resting state.

PubMed

Hansen, Enrique C A; Battaglia, Demian; Spiegler, Andreas; Deco, Gustavo; Jirsa, Viktor K

2015-01-15

Functional connectivity (FC) sheds light on the interactions between different brain regions. Besides basic research, it is clinically relevant for applications in Alzheimer's disease, schizophrenia, presurgical planning, epilepsy, and traumatic brain injury. Simulations of whole-brain mean-field computational models with realistic connectivity determined by tractography studies enable us to reproduce with accuracy aspects of average FC in the resting state. Most computational studies, however, did not address the prominent non-stationarity in resting state FC, which may result in large intra- and inter-subject variability and thus preclude an accurate individual predictability. Here we show that this non-stationarity reveals a rich structure, characterized by rapid transitions switching between a few discrete FC states. We also show that computational models optimized to fit time-averaged FC do not reproduce these spontaneous state transitions and, thus, are not qualitatively superior to simplified linear stochastic models, which account for the effects of structure alone. We then demonstrate that a slight enhancement of the non-linearity of the network nodes is sufficient to broaden the repertoire of possible network behaviors, leading to modes of fluctuations, reminiscent of some of the most frequently observed Resting State Networks. Because of the noise-driven exploration of this repertoire, the dynamics of FC qualitatively change now and display non-stationary switching similar to empirical resting state recordings (Functional Connectivity Dynamics (FCD)). Thus FCD bear promise to serve as a better biomarker of resting state neural activity and of its pathologic alterations. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Photophysics of phenol and pentafluorophenol: The role of nonadiabaticity in the optical transition to the lowest bright 1ππ* state

NASA Astrophysics Data System (ADS)

Rajak, Karunamoy; Ghosh, Arpita; Mahapatra, S.

2018-02-01

We report multimode vibronic coupling of the energetically low-lying electronic states of phenol and pentafluorophenol in this article. First principles nuclear dynamics calculations are carried out to elucidate the optical absorption spectrum of both of the molecules. This is motivated by the recent experimental measurements [S. Karmakar et al., J. Chem. Phys. 142, 184303 (2015)] on these systems. Diabatic vibronic coupling models are developed with the aid of adiabatic electronic energies calculated ab initio by the equation of motion coupled cluster quantum chemistry method. A nuclear dynamics study on the constructed electronic states is carried out by both the time-independent and time-dependent quantum mechanical methods. It is found that the nature of low-energy πσ* transition changes, and in pentafluorophenol the energy of the first two 1πσ* states, is lowered by about half an eV (vertically, relative to those in phenol), and they become energetically close to the optically bright first excited 1ππ* (S1) state. This results in strong vibronic coupling and multiple multi-state conical intersections among the ππ* and πσ* electronic states of pentafluorophenol. The impact of associated nonadiabatic effects on the vibronic structure and dynamics of the 1ππ* state is examined at length. The structured vibronic band of phenol becomes structureless in pentafluorophenol. The theoretical results are found to be in good accord with the experimental finding at both high energy resolution and low energy resolution.

Constant pH simulations of pH responsive polymers

NASA Astrophysics Data System (ADS)

Sharma, Arjun; Smith, J. D.; Walters, Keisha B.; Rick, Steven W.

2016-12-01

Polyacidic polymers can change structure over a narrow range of pH in a competition between the hydrophobic effect, which favors a compact state, and electrostatic repulsion, which favors an extended state. Constant pH molecular dynamics computer simulations of poly(methacrylic acid) reveal that there are two types of structural changes, one local and one global, which make up the overall response. The local structural response depends on the tacticity of the polymer and leads to different cooperative effects for polymers with different stereochemistries, demonstrating both positive and negative cooperativities.

A stochastic global identification framework for aerospace structures operating under varying flight states

NASA Astrophysics Data System (ADS)

Kopsaftopoulos, Fotis; Nardari, Raphael; Li, Yu-Hung; Chang, Fu-Kuo

2018-01-01

In this work, a novel data-based stochastic "global" identification framework is introduced for aerospace structures operating under varying flight states and uncertainty. In this context, the term "global" refers to the identification of a model that is capable of representing the structure under any admissible flight state based on data recorded from a sample of these states. The proposed framework is based on stochastic time-series models for representing the structural dynamics and aeroelastic response under multiple flight states, with each state characterized by several variables, such as the airspeed, angle of attack, altitude and temperature, forming a flight state vector. The method's cornerstone lies in the new class of Vector-dependent Functionally Pooled (VFP) models which allow the explicit analytical inclusion of the flight state vector into the model parameters and, hence, system dynamics. This is achieved via the use of functional data pooling techniques for optimally treating - as a single entity - the data records corresponding to the various flight states. In this proof-of-concept study the flight state vector is defined by two variables, namely the airspeed and angle of attack of the vehicle. The experimental evaluation and assessment is based on a prototype bio-inspired self-sensing composite wing that is subjected to a series of wind tunnel experiments under multiple flight states. Distributed micro-sensors in the form of stretchable sensor networks are embedded in the composite layup of the wing in order to provide the sensing capabilities. Experimental data collected from piezoelectric sensors are employed for the identification of a stochastic global VFP model via appropriate parameter estimation and model structure selection methods. The estimated VFP model parameters constitute two-dimensional functions of the flight state vector defined by the airspeed and angle of attack. The identified model is able to successfully represent the wing's aeroelastic response under the admissible flight states via a minimum number of estimated parameters compared to standard identification approaches. The obtained results demonstrate the high accuracy and effectiveness of the proposed global identification framework, thus constituting a first step towards the next generation of "fly-by-feel" aerospace vehicles with state awareness capabilities.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

NASA Astrophysics Data System (ADS)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-09-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlapmore » with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.« less

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

PubMed Central

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-01-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space. PMID:25240340

Atomic and electronic structure transformations of silver nanoparticles under rapid cooling conditions.

PubMed

Lobato, I; Rojas, J; Landauro, C V; Torres, J

2009-02-04

The structural evolution and dynamics of silver nanodrops Ag(2869) (4.4 nm in diameter) under rapid cooling conditions have been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modelled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique are used to reveal the structural transition in the process of solidification. It is shown that Ag nanoparticles evolve into different nanostructures under different cooling processes. At a cooling rate of 1.5625 × 10(13) K s(-1) the nanoparticles preserve an amorphous-like structure containing a large amount of 1551 and 1541 pairs which correspond to icosahedral symmetry. For a lower cooling rate (1.5625 × 10(12) K s(-1)), the nanoparticles transform into a crystal-like structure consisting mainly of 1421 and 1422 pairs which correspond to the face centred cubic and hexagonal close packed structures, respectively. The variations of the electronic density of states for the differently cooled nanoparticles are small, but in correspondence with the structural changes.

Dynamic response and transfer function of social systems: A neuro-inspired model of collective human activity patterns.

PubMed

Lymperopoulos, Ilias N

2017-10-01

The interaction of social networks with the external environment gives rise to non-stationary activity patterns reflecting the temporal structure and strength of exogenous influences that drive social dynamical processes far from an equilibrium state. Following a neuro-inspired approach, based on the dynamics of a passive neuronal membrane, and the firing rate dynamics of single neurons and neuronal populations, we build a state-of-the-art model of the collective social response to exogenous interventions. In this regard, we analyze online activity patterns with a view to determining the transfer function of social systems, that is, the dynamic relationship between external influences and the resulting activity. To this end, first we estimate the impulse response (Green's function) of collective activity, and then we show that the convolution of the impulse response with a time-varying external influence field accurately reproduces empirical activity patterns. To capture the dynamics of collective activity when the generating process is in a state of statistical equilibrium, we incorporate into the model a noisy input convolved with the impulse response function, thus precisely reproducing the fluctuations of stationary collective activity around a resting value. The outstanding goodness-of-fit of the model results to empirical observations, indicates that the model explains human activity patterns generated by time-dependent external influences in various socio-economic contexts. The proposed model can be used for inferring the temporal structure and strength of external influences, as well as the inertia of collective social activity. Furthermore, it can potentially predict social activity patterns. Copyright © 2017 Elsevier Ltd. All rights reserved.

Excited-State Deactivation of Branched Phthalocyanine Compounds.

PubMed

Zhu, Huaning; Li, Yang; Chen, Jun; Zhou, Meng; Niu, Yingli; Zhang, Xinxing; Guo, Qianjin; Wang, Shuangqing; Yang, Guoqiang; Xia, Andong

2015-12-21

The excited-state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis- and trisphthalocyanines) are studied by using steady-state and femtosecond transient absorption spectral measurements, where the excited-state energy-transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis-Pc). In trisphthalocyanine (tris-Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre-associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady-state spectra also show a face-to-face conformation in bis-Pc, whereas in tris-Pc, two of the three phthalocyanine branches form a pre-associated face-to-face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure-property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Excitonic enhancement of nonradiative energy transfer to bulk silicon with the hybridization of cascaded quantum dots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yeltik, Aydan; Guzelturk, Burak; Akhavan, Shahab

2013-12-23

We report enhanced sensitization of silicon through nonradiative energy transfer (NRET) of the excitons in an energy-gradient structure composed of a cascaded bilayer of green- and red-emitting CdTe quantum dots (QDs) on bulk silicon. Here NRET dynamics were systematically investigated comparatively for the cascaded energy-gradient and mono-dispersed QD structures at room temperature. We show experimentally that NRET from the QD layer into silicon is enhanced by 40% in the case of an energy-gradient cascaded structure as compared to the mono-dispersed structures, which is in agreement with the theoretical analysis based on the excited state population-depopulation dynamics of the QDs.

Roton Excitations and the Fluid-Solid Phase Transition in Superfluid 2D Yukawa Bosons

NASA Astrophysics Data System (ADS)

Molinelli, S.; Galli, D. E.; Reatto, L.; Motta, M.

2016-10-01

We compute several ground-state properties and the dynamical structure factor of a zero-temperature system of Bosons interacting with the 2D screened Coulomb (2D-SC) potential. We resort to the exact shadow path integral ground state (SPIGS) quantum Monte Carlo method to compute the imaginary-time correlation function of the model, and to the genetic algorithm via falsification of theories (GIFT) to retrieve the dynamical structure factor. We provide a detailed comparison of ground-state properties and collective excitations of 2D-SC and ^4He atoms. The roton energy of the 2D-SC system is an increasing function of density, and not a decreasing one as in ^4He. This result is in contrast with the view that the roton is the soft mode of the fluid-solid transition. We uncover a remarkable quasi-universality of backflow and of other properties when expressed in terms of the amount of short-range order as quantified by the height of the first peak of the static structure factor.

Mechanism of extracellular ion exchange and binding-site occlusion in the sodium-calcium exchanger

PubMed Central

Lee, ChangKeun; Huang, Yihe; Faraldo-Gómez, José D.; Jiang, Youxing

2016-01-01

Na+/Ca2+ exchangers utilize the Na+ electrochemical gradient across the plasma membrane to extrude intracellular Ca2+, and play a central role in Ca2+ homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na+, Ca2+ or Sr2+ in various occupancies and in an apo state. This analysis defines the binding mode and relative affinity of these ions, establishes the structural basis for the anticipated 3Na+:1Ca2+ exchange stoichiometry, and reveals the conformational changes at the onset of the alternating-access transport mechanism. An independent analysis of the dynamics and conformational free-energy landscape of NCX_Mj in different ion-occupancy states, based on enhanced-sampling molecular-dynamics simulations, demonstrates that the crystal structures reflect mechanistically relevant, interconverting conformations. These calculations also reveal the mechanism by which the outward-to-inward transition is controlled by the ion-occupancy state, thereby explaining the emergence of strictly-coupled Na+/Ca2+ antiport. PMID:27183196

Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger

DOE PAGES

Liao, Jun; Marinelli, Fabrizio; Lee, Changkeun; ...

2016-05-16

Na +/Ca 2+ exchangers utilize the Na + electrochemical gradient across the plasma membrane to extrude intracellular Ca 2+, and play a central role in Ca 2+ homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na +, Ca 2+ or Sr 2+ in various occupancies and in an apo state. This analysis defines the binding mode and relative affinity of these ions, establishes the structural basis for the anticipated 3:1Na +/Ca 2+ exchange stoichiometry, and reveals the conformational changes at the onset ofmore » the alternating-access transport mechanism. An independent analysis of the dynamics and conformational free-energy landscape of NCX_Mj in different ion-occupancy states, based on enhanced-sampling molecular-dynamics simulations, demonstrates that the crystal structures reflect mechanistically relevant, interconverting conformations. Lastly, these calculations also reveal the mechanism by which the outward-to-inward transition is controlled by the ion-occupancy state, thereby explaining the emergence of strictly-coupled Na +/Ca 2+ antiport.« less

Sleep Neurophysiological Dynamics Through the Lens of Multitaper Spectral Analysis

PubMed Central

Prerau, Michael J.; Brown, Ritchie E.; Bianchi, Matt T.; Ellenbogen, Jeffrey M.; Purdon, Patrick L.

2016-01-01

During sleep, cortical and subcortical structures within the brain engage in highly structured oscillatory dynamics that can be observed in the electroencephalogram (EEG). The ability to accurately describe changes in sleep state from these oscillations has thus been a major goal of sleep medicine. While numerous studies over the past 50 years have shown sleep to be a continuous, multifocal, dynamic process, long-standing clinical practice categorizes sleep EEG into discrete stages through visual inspection of 30-s epochs. By representing sleep as a coarsely discretized progression of stages, vital neurophysiological information on the dynamic interplay between sleep and arousal is lost. However, by using principled time-frequency spectral analysis methods, the rich dynamics of the sleep EEG are immediately visible—elegantly depicted and quantified at time scales ranging from a full night down to individual microevents. In this paper, we review the neurophysiology of sleep through this lens of dynamic spectral analysis. We begin by reviewing spectral estimation techniques traditionally used in sleep EEG analysis and introduce multitaper spectral analysis, a method that makes EEG spectral estimates clearer and more accurate than traditional approaches. Through the lens of the multitaper spectrogram, we review the oscillations and mechanisms underlying the traditional sleep stages. In doing so, we will demonstrate how multitaper spectral analysis makes the oscillatory structure of traditional sleep states instantaneously visible, closely paralleling the traditional hypnogram, but with a richness of information that suggests novel insights into the neural mechanisms of sleep, as well as novel clinical and research applications. PMID:27927806

Dynamics of dissipative self-assembly of particles interacting through oscillatory forces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tagliazucchi, M.; Szleifer, I.

Dissipative self-assembly is the formation of ordered structures far from equilibrium, which continuously uptake energy and dissipate it into the environment. Due to its dynamical nature, dissipative self-assembly can lead to new phenomena and possibilities of self-organization that are unavailable to equilibrium systems. Understanding the dynamics of dissipative self-assembly is required in order to direct the assembly to structures of interest. In the present work, Brownian dynamics simulations and analytical theory were used to study the dynamics of self-assembly of a mixture of particles coated with weak acids and bases under continuous oscillations of the pH. The pH of themore » system modulates the charge of the particles and, therefore, the interparticle forces oscillate in time. This system produces a variety of self-assembled structures, including colloidal molecules, fibers and different types of crystalline lattices. The most important conclusions of our study are: (i) in the limit of fast oscillations, the whole dynamics (and not only those at the non-equilibrium steady state) of a system of particles interacting through time-oscillating interparticle forces can be described by an effective potential that is the time average of the time-dependent potential over one oscillation period; (ii) the oscillation period is critical to determine the order of the system. In some cases the order is favored by very fast oscillations while in others small oscillation frequencies increase the order. In the latter case, it is shown that slow oscillations remove kinetic traps and, thus, allow the system to evolve towards the most stable non-equilibrium steady state.« less

Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding.

PubMed

Singh, Priya; Choudhury, Susobhan; Dutta, Shreyasi; Adhikari, Aniruddha; Bhattacharya, Siddhartha; Pal, Debasish; Pal, Samir Kumar

2017-10-01

The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG. We have also labelled the enzyme by a well-known fluorescent probe 8-anilino-1-naphthalenesulfonic acid ammonium salt (ANS) to study the molecular mechanism of the protein-DNA association through exited state relaxation of the probe in absence (dictated by polarity) and presence of EB in the DNA (dictated by Förster resonance energy transfer (FRET)). The overall and local structures of the protein in presence of PEG have been followed by circular dichroism and time resolved polarization gated spectroscopy respectively. The enhanced dynamical flexibility of protein in presence of PEG as revealed from excited state lifetime and polarization gated anisotropy of ANS has been correlated with the stronger DNA-binding for the higher nuclease activity. We have also used conventional experimental strategy of agarose gel electrophoresis to monitor DNA-cleavage and found consistent results of enhanced nuclease activities both on synthetic 20-mer oligonucleotide and long genomic DNA from calf thymus. Copyright © 2017 Elsevier B.V. All rights reserved.

Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example.

PubMed

Liu, Jiaojiao; Dai, Jin; He, Jianfeng; Niemi, Antti J; Ilieva, Nevena

2017-03-01

We propose to combine a mean-field approach with all-atom molecular dynamics (MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques. We argue that a room-temperature monomeric Myc is in a dynamical state, it oscillates between different conformations that we identify. For this we adopt the Cα backbone of Myc in a crystallographic heteromer as an initial ansatz for the monomeric structure. We construct a multisoliton of the pertinent Landau free energy to describe the Cα profile with ultrahigh precision. We use Glauber dynamics to resolve how the multisoliton responds to repeated increases and decreases in ambient temperature. We confirm that the initial structure is unstable in isolation. We reveal a highly degenerate ground-state landscape, an attractive set towards which Glauber dynamics converges in the limit of vanishing ambient temperature. We analyze the thermal stability of this Glauber attractor using room-temperature molecular dynamics. We identify and scrutinize a particularly stable subset in which the two helical segments of the original multisoliton align in parallel next to each other. During the MD time evolution of a representative structure from this subset, we observe intermittent quasiparticle oscillations along the C-terminal α helix, some of which resemble a translating Davydov's Amide-I soliton. We propose that the presence of oscillatory motion is in line with the expected intrinsically disordered character of Myc.

Recent Advances and Applications in Synchrotron X-Ray Protein Footprinting for Protein Structure and Dynamics Elucidation.

PubMed

Gupta, Sayan; Feng, Jun; Chance, Mark; Ralston, Corie

2016-01-01

Synchrotron X-ray Footprinting is a powerful in situ hydroxyl radical labeling method for analysis of protein structure, interactions, folding and conformation change in solution. In this method, water is ionized by high flux density broad band synchrotron X-rays to produce a steady-state concentration of hydroxyl radicals, which then react with solvent accessible side-chains. The resulting stable modification products are analyzed by liquid chromatography coupled to mass spectrometry. A comparative reactivity rate between known and unknown states of a protein provides local as well as global information on structural changes, which is then used to develop structural models for protein function and dynamics. In this review we describe the XF-MS method, its unique capabilities and its recent technical advances at the Advanced Light Source. We provide a comparison of other hydroxyl radical and mass spectrometry based methods with XFMS. We also discuss some of the latest developments in its usage for studying bound water, transmembrane proteins and photosynthetic protein components, and the synergy of the method with other synchrotron based structural biology methods.

Crystal structure, conformational analysis, and molecular dynamics of tetra-0-methyl-(+)-catechin

Treesearch

Frank R. Fronczek; Richard W. Hemingway; G. Wayne McGraw; Jan P. Steynberg; Carin A. Helfer; Wayne L. Mattice

1993-01-01

The structure of tetra-O-methyl-(+)-catechin has been determined in the crystalline state. Two independent molecules, denoted structure A and structure B, exist in the unit cell. Crystals are triclinic, space group P1, a=4.8125(2) Ǻ, b=12.9148(8) Ǻ, c=13.8862(11) Ǻ, α=86.962(6)°, β=89.120(5)°, γ=...

NMR structural and dynamic characterization of the acid-unfolded state of apomyoglobin provides insights into the early events in protein folding.

PubMed

Yao, J; Chung, J; Eliezer, D; Wright, P E; Dyson, H J

2001-03-27

Apomyoglobin forms a denatured state under low-salt conditions at pH 2.3. The conformational propensities and polypeptide backbone dynamics of this state have been characterized by NMR. Nearly complete backbone and some side chain resonance assignments have been obtained, using a triple-resonance assignment strategy tailored to low protein concentration (0.2 mM) and poor chemical shift dispersion. An estimate of the population and location of residual secondary structure has been made by examining deviations of (13)C(alpha), (13)CO, and (1)H(alpha) chemical shifts from random coil values, scalar (3)J(HN,H)(alpha) coupling constants and (1)H-(1)H NOEs. Chemical shifts constitute a highly reliable indicator of secondary structural preferences, provided the appropriate random coil chemical shift references are used, but in the case of acid-unfolded apomyoglobin, (3)J(HN,H)(alpha) coupling constants are poor diagnostics of secondary structure formation. Substantial populations of helical structure, in dynamic equilibrium with unfolded states, are formed in regions corresponding to the A and H helices of the folded protein. In addition, the deviation of the chemical shifts from random coil values indicates the presence of helical structure encompassing the D helix and extending into the first turn of the E helix. The polypeptide backbone dynamics of acid-unfolded apomyoglobin have been investigated using reduced spectral density function analysis of (15)N relaxation data. The spectral density J(omega(N)) is particularly sensitive to variations in backbone fluctuations on the picosecond to nanosecond time scale. The central region of the polypeptide spanning the C-terminal half of the E helix, the EF turn, and the F helix behaves as a free-flight random coil chain, but there is evidence from J(omega(N)) of restricted motions on the picosecond to nanosecond time scale in the A and H helix regions where there is a propensity to populate helical secondary structure in the acid-unfolded state. Backbone fluctuations are also restricted in parts of the B and G helices due to formation of local hydrophobic clusters. Regions of restricted backbone flexibility are generally associated with large buried surface area. A significant increase in J(0) is observed for the NH resonances of some residues located in the A and G helices of the folded protein and is associated with fluctuations on a microsecond to millisecond time scale that probably arise from transient contacts between these distant regions of the polypeptide chain. Our results indicate that the equilibrium unfolded state of apomyoglobin formed at pH 2.3 is an excellent model for the events that are expected to occur in the earliest stages of protein folding, providing insights into the regions of the polypeptide that spontaneously undergo local hydrophobic collapse and sample nativelike secondary structure.

The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.

PubMed

Duchi, Diego; Mazumder, Abhishek; Malinen, Anssi M; Ebright, Richard H; Kapanidis, Achillefs N

2018-06-06

RNA polymerase (RNAP) contains a mobile structural module, the 'clamp,' that forms one wall of the RNAP active-center cleft and that has been linked to crucial aspects of the transcription cycle, including promoter melting, transcription elongation complex stability, transcription pausing, and transcription termination. Using single-molecule FRET on surface-immobilized RNAP molecules, we show that the clamp in RNAP holoenzyme populates three distinct conformational states and interconvert between these states on the 0.1-1 s time-scale. Similar studies confirm that the RNAP clamp is closed in open complex (RPO) and in initial transcribing complexes (RPITC), including paused initial transcribing complexes, and show that, in these complexes, the clamp does not exhibit dynamic behaviour. We also show that, the stringent-response alarmone ppGpp, which reprograms transcription during amino acid starvation stress, selectively stabilizes the partly-closed-clamp state and prevents clamp opening; these results raise the possibility that ppGpp controls promoter opening by modulating clamp dynamics.

Side-chain mobility in the folded state of Myoglobin

NASA Astrophysics Data System (ADS)

Lammert, Heiko; Onuchic, Jose

We study the accessibility of alternative side-chain rotamer configurations in the native state of Myoglobin, using an all-atom structure-based model. From long, unbiased simulation trajectories we determine occupancies of rotameric states and also estimate configurational and vibrational entropies. Direct sampling of the full native-state dynamics, enabled by the simple model, reveals facilitation of side-chain motions by backbone dynamics. Correlations between different dihedral angles are quantified and prove to be weak. We confirm global trends in the mobilities of side-chains, following burial and also the chemical character of residues. Surface residues loose little configurational entropy upon folding; side-chains contribute significantly to the entropy of the folded state. Mobilities of buried side-chains vary strongly with temperature. At ambient temperature, individual side-chains in the core of the protein gain substantial access to alternative rotamers, with occupancies that are likely observable experimentally. Finally, the dynamics of buried side-chains may be linked to the internal pockets, available to ligand gas molecules in Myoglobin.

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems

NASA Astrophysics Data System (ADS)

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; Del Giudice, Paolo

2015-10-01

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a ‘basin’ of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases.

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems.

PubMed

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; del Giudice, Paolo

2015-10-14

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a 'basin' of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases.

Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulations.

PubMed

Loccisano, Anne E; Acevedo, Orlando; DeChancie, Jason; Schulze, Brita G; Evanseck, Jeffrey D

2004-05-01

The utility of multiple trajectories to extend the time scale of molecular dynamics simulations is reported for the spectroscopic A-states of carbonmonoxy myoglobin (MbCO). Experimentally, the A0-->A(1-3) transition has been observed to be 10 micros at 300 K, which is beyond the time scale of standard molecular dynamics simulations. To simulate this transition, 10 short (400 ps) and two longer time (1.2 ns) molecular dynamics trajectories, starting from five different crystallographic and solution phase structures with random initial velocities centered in a 37 A radius sphere of water, have been used to sample the native-fold of MbCO. Analysis of the ensemble of structures gathered over the cumulative 5.6 ns reveals two biomolecular motions involving the side chains of His64 and Arg45 to explain the spectroscopic states of MbCO. The 10 micros A0-->A(1-3) transition involves the motion of His64, where distance between His64 and CO is found to vary up to 8.8 +/- 1.0 A during the transition of His64 from the ligand (A(1-3)) to bulk solvent (A0). The His64 motion occurs within a single trajectory only once, however the multiple trajectories populate the spectroscopic A-states fully. Consequently, multiple independent molecular dynamics simulations have been found to extend biomolecular motion from 5 ns of total simulation to experimental phenomena on the microsecond time scale.

Simulations of submonolayer Xe on Pt(111): The case for a chaotic low temperature phase

NASA Astrophysics Data System (ADS)

Novaco, Anthony D.; Bavaresco, Jessica

2018-04-01

Molecular dynamics simulations are reported for the structural and thermodynamic properties of submonolayer xenon adsorbed on the (111) surface of platinum for temperatures up to the (apparently incipient) triple point and beyond. While the motion of the atoms in the surface plane is treated with a standard two-dimensional molecular dynamics simulation, the model takes into consideration the thermal excitation of quantum states associated with surface-normal dynamics in an attempt to describe the apparent smoothing of the corrugation with increasing temperature. We examine the importance of this thermal smoothing to the relative stability of several observed and proposed low-temperature structures. Structure factor calculations are compared to experimental results in an attempt to determine the low temperature structure of this system. These calculations provide strong evidence that, at very low temperatures, the domain wall structure of a xenon monolayer adsorbed on a Pt(111) substrate possesses a chaotic-like nature, exhibiting long-lived meta-stable states with pinned domain walls, these walls having narrow widths and irregular shapes. This result is contrary to the standard wisdom regarding this system, namely, that the very low temperature phase of this system is a striped incommensurate phase. We present the case for further experimental investigation of this and similar systems as possible examples of chaotic low temperature phases in two dimensions.

Structure of Alzheimer's 10-35 β peptide from replica-exchange molecular dynamics simulations in explicit water

NASA Astrophysics Data System (ADS)

Baumketner, Andriy; Shea, Joan-Emma

2006-03-01

We report a replica-exchange molecular dynamics study of the 10-35 fragment of Alzheimer's disease amyloid β peptide, Aβ10-35, in aqueous solution. This fragment was previously seen [J. Str. Biol. 130 (2000) 130] to possess all the most important amyloidogenic properties characteristic of full-length Aβ peptides. Our simulations attempted to fold Aβ10-35 from first principles. The peptide was modeled using all-atom OPLS/AA force field in conjunction with the TIP3P explicit solvent model. A total of 72 replicas were considered and simulated over 40 ns of total time, including 5 ns of initial equilibration. We find that Aβ10-35 does not possess any unique folded state, a 3D structure of predominant population, under normal temperature and pressure. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is seen to be dominated by random coil and bend structures with insignificant presence of α-helical or β-sheet structure. We find that, overall, the 3D structure of Aβ10-35 is shaped by salt bridges formed between oppositely charged residues.Of all possible salt bridges, K28-D23 was seen to have the highest formation probability, totaling more than 60% of the time.

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.

PubMed

Tomić, A; Berynskyy, M; Wade, R C; Tomić, S

2015-11-01

The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.

The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion.

PubMed

Lin, Mary G; Schöneberg, Johannes; Davies, Christopher W; Ren, Xuefeng; Hurley, James H

2018-05-15

Yeast macroautophagy begins with the de novo formation of a double-membrane phagophore at the preautophagosomal structure/phagophore assembly site (PAS), followed by its expansion into the autophagosome responsible for cargo engulfment. The kinase Atg1 is recruited to the PAS by Atg13 through interactions between the EAT domain of the former and the tMIM motif of the latter. Mass-spectrometry data have shown that, in the absence of Atg13, the EAT domain structure is strikingly dynamic, but the function of this Atg13-free dynamic state has been unclear. We used structure-based mutational analysis and quantitative and superresolution microscopy to show that Atg1 is present on autophagic puncta at, on average, twice the stoichiometry of Atg13. Moreover, Atg1 colocalizes with the expanding autophagosome in a manner dependent on Atg8 but not Atg13. We used isothermal titration calorimetry and crystal structure information to design an EAT domain mutant allele ATG1 DD that selectively perturbs the function of the Atg13-free state. Atg1 DD shows reduced PAS formation and does not support phagophore expansion, showing that the EAT domain has an essential function that is separate from its Atg13-dependent role in autophagy initiation.

Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding

PubMed Central

Tajima, Satohiro; Yanagawa, Toru; Fujii, Naotaka; Toyoizumi, Taro

2015-01-01

Brain-wide interactions generating complex neural dynamics are considered crucial for emergent cognitive functions. However, the irreducible nature of nonlinear and high-dimensional dynamical interactions challenges conventional reductionist approaches. We introduce a model-free method, based on embedding theorems in nonlinear state-space reconstruction, that permits a simultaneous characterization of complexity in local dynamics, directed interactions between brain areas, and how the complexity is produced by the interactions. We demonstrate this method in large-scale electrophysiological recordings from awake and anesthetized monkeys. The cross-embedding method captures structured interaction underlying cortex-wide dynamics that may be missed by conventional correlation-based analysis, demonstrating a critical role of time-series analysis in characterizing brain state. The method reveals a consciousness-related hierarchy of cortical areas, where dynamical complexity increases along with cross-area information flow. These findings demonstrate the advantages of the cross-embedding method in deciphering large-scale and heterogeneous neuronal systems, suggesting a crucial contribution by sensory-frontoparietal interactions to the emergence of complex brain dynamics during consciousness. PMID:26584045

Pressure Studies of Protein Dynamics.

DTIC Science & Technology

1987-02-20

applicable ) Office of Naval Research ONR N00014-86-K-0270 kc. ADDRESS (City, State,and ZIP Code) 10. SOURCE OF FUNDING NUMBERS - PROGRAM PROJECT I TASK IWORK...Pressure Studies of Protein Dynamics 12. PERSONAL AUTHOR(S) Hans Frauenfelder and Robert D. Young 13a. TYPE OF REPORT |13b. TIME COVERED 114 DATE OF...relatioihbetween dynamic structure and function of protein protein dyna -bsey observing the phenomena induced by flash photolysis using near ultravfilet

Molecular Dynamics Simulation of Telomere and TRF1

NASA Astrophysics Data System (ADS)

Kaburagi, Masaaki; Fukuda, Masaki; Yamada, Hironao; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako; Kato, Takamitsu A.; Uesaka, Mitsuru

Telomeres play a central role in determining longevity of a cell. Our study focuses on the interaction between telomeric guanines and TRF1 as a means to observe the telomeric based mechanism of the genome protection. In this research, we performed molecular dynamics simulations of a telomeric DNA and TRF1. Our results show a stable structure with a high affinity for the specific protein. Additionally, we calculated the distance between guanines and the protein in their complex state. From this comparison, we found the calculated values of distance to be very similar, and the angle of guanines in their complex states was larger than that in their single state.

Subpicosecond X rotations of atomic clock states

NASA Astrophysics Data System (ADS)

Song, Yunheung; Lee, Han-gyeol; Kim, Hyosub; Jo, Hanlae; Ahn, Jaewook

2018-05-01

We demonstrate subpicosecond-timescale population transfer between the pair of hyperfine ground states of atomic rubidium using a single laser-pulse. Our scheme utilizes the geometric and dynamic phases induced during Rabi oscillation through the fine-structure excited state to construct an X rotation gate for the hyperfine-state qubit system. The experiment performed with a femtosecond laser and cold rubidium atoms, in a magnetooptical trap, shows over 98% maximal population transfer between the clock states.

Heterogeneous chain dynamics and aggregate lifetimes in precise acid-containing polyethylenes: Experiments and simulations

DOE PAGES

Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph; ...

2016-11-10

Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.

PubMed

Spyrakis, Francesca; Benedetti, Paolo; Decherchi, Sergio; Rocchia, Walter; Cavalli, Andrea; Alcaro, Stefano; Ortuso, Francesco; Baroni, Massimo; Cruciani, Gabriele

2015-10-26

The importance of taking into account protein flexibility in drug design and virtual ligand screening (VS) has been widely debated in the literature, and molecular dynamics (MD) has been recognized as one of the most powerful tools for investigating intrinsic protein dynamics. Nevertheless, deciphering the amount of information hidden in MD simulations and recognizing a significant minimal set of states to be used in virtual screening experiments can be quite complicated. Here we present an integrated MD-FLAP (molecular dynamics-fingerprints for ligand and proteins) approach, comprising a pipeline of molecular dynamics, clustering and linear discriminant analysis, for enhancing accuracy and efficacy in VS campaigns. We first extracted a limited number of representative structures from tens of nanoseconds of MD trajectories by means of the k-medoids clustering algorithm as implemented in the BiKi Life Science Suite ( http://www.bikitech.com [accessed July 21, 2015]). Then, instead of applying arbitrary selection criteria, that is, RMSD, pharmacophore properties, or enrichment performances, we allowed the linear discriminant analysis algorithm implemented in FLAP ( http://www.moldiscovery.com [accessed July 21, 2015]) to automatically choose the best performing conformational states among medoids and X-ray structures. Retrospective virtual screenings confirmed that ensemble receptor protocols outperform single rigid receptor approaches, proved that computationally generated conformations comprise the same quantity/quality of information included in X-ray structures, and pointed to the MD-FLAP approach as a valuable tool for improving VS performances.

Optimal control on hybrid ode systems with application to a tick disease model.

PubMed

Ding, Wandi

2007-10-01

We are considering an optimal control problem for a type of hybrid system involving ordinary differential equations and a discrete time feature. One state variable has dynamics in only one season of the year and has a jump condition to obtain the initial condition for that corresponding season in the next year. The other state variable has continuous dynamics. Given a general objective functional, existence, necessary conditions and uniqueness for an optimal control are established. We apply our approach to a tick-transmitted disease model with age structure in which the tick dynamics changes seasonally while hosts have continuous dynamics. The goal is to maximize disease-free ticks and minimize infected ticks through an optimal control strategy of treatment with acaricide. Numerical examples are given to illustrate the results.

Temporal dynamics and population genetic structure of Fusarium graminearum in the upper Midwestern United States

USDA-ARS?s Scientific Manuscript database

Fusarium graminearum sensu stricto causes Fusarium head blight (FHB) in wheat and barley, and contaminates grains with several trichothecene mycotoxins, causing destructive yield losses and economic impact in the United States. Recently, a F. graminearum strain collected from Minnesota (MN) was dete...