Página 1 dos resultados de 10060 itens digitais encontrados em 0.029 segundos

A contribution for nonlinear structural dynamics characterization of cantilever beams

Barros, Everaldo de; Mathias, Mauro Hugo
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Conferência ou Objeto de Conferência Formato: 1950-1959
ENG
Relevância na Pesquisa
55.95%
Successful experiments in nonlinear vibrations have been carried out with cantilever beams under harmonic base excitation. A flexible slender cantilever has been chosen as a convenient structure to exhibit modal interactions, subharmonic, superharmonic and chaotic motions, and others interesting nonlinear phenomena. The tools employed to analyze the dynamics of the beam generally include frequency- and force-response curves. To produce force-response curves, one keeps the excitation frequency constant and slowly varies the excitation amplitude, on the other hand, to produce frequency-response curves, one keeps the excitation amplitude fixed and slowly varies the excitation frequency. However, keeping the excitation amplitude constant while varying the excitation frequency is a difficult task with an open-loop measurement system. In this paper, it is proposed a closed-loop monitor vibration system available with the electromagnetic shaker in order to keep the harmonic base excitation amplitude constant. This experimental setup constitutes a significant improvement to produce frequency-response curves and the advantages of this setup are evaluated in a case study. The beam is excited with a periodic base motion transverse to the axis of the beam near the third natural frequency. Modal interactions and two-period quasi-periodic motion are observed involving the first and the third modes. Frequency-response curves...

Structural dynamics of the lac repressor–DNA complex revealed by a multiscale simulation

Villa, Elizabeth; Balaeff, Alexander; Schulten, Klaus
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.91%
A multiscale simulation of a complex between the lac repressor protein (LacI) and a 107-bp-long DNA segment is reported. The complex between the repressor and two operator DNA segments is described by all-atom molecular dynamics; the size of the simulated system comprises either 226,000 or 314,000 atoms. The DNA loop connecting the operators is modeled as a continuous elastic ribbon, described mathematically by the nonlinear Kirchhoff differential equations with boundary conditions obtained from the coordinates of the terminal base pairs of each operator. The forces stemming from the looped DNA are included in the molecular dynamics simulations; the loop structure and the forces are continuously recomputed because the protein motions during the simulations shift the operators and the presumed termini of the loop. The simulations reveal the structural dynamics of the LacI–DNA complex in unprecedented detail. The multiple domains of LacI exhibit remarkable structural stability during the simulation, moving much like rigid bodies. LacI is shown to absorb the strain from the looped DNA mainly through its mobile DNA-binding head groups. Even with large fluctuating forces applied, the head groups tilt strongly and keep their grip on the operator DNA...

Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography

Bourgeois, Dominique; Vallone, Beatrice; Arcovito, Alessandro; Sciara, Giuliano; Schotte, Friedrich; Anfinrud, Philip A.; Brunori, Maurizio
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.99%
Work carried out over the last 30 years unveiled the role of structural dynamics in controlling protein function. Cavity networks modulate structural dynamics trajectories and are functionally relevant; in globins they have been assigned a role in ligand migration and docking. These findings raised renewed interest for time-resolved structural investigations of myoglobin (Mb), a simple heme protein displaying a photosensitive iron-ligand bond. Photodissociation of MbCO generates a nonequilibrium population of protein structures relaxing over a time range extending from picoseconds to milliseconds. This process triggers ligand migration to matrix cavities with clear-cut effects on the rate and yield of geminate rebinding. Here, we report subnanosecond time-resolved Laue diffraction data on the triple mutant YQR-Mb [Leu-29(B10)Tyr, His-64(E7)Gln, Thr-67(E10)Arg] that depict the sequence of structural events associated with heme and protein relaxation from 100 ps to 316 ns and above. The photodissociated ligand rapidly (<0.1 ns) populates the Xe-binding cavity distal to the heme. Moreover, the heme relaxation toward the deoxy configuration is heterogeneous, with a slower phase (≈ns) evident in these experiments. Damping of the heme response appears to result from a strain exerted by the E-helix via the CD-turn; Phe-43(CD1)...

A combined structural dynamics approach identifies a putative switch in factor VIIa employed by tissue factor to initiate blood coagulation

Olsen, Ole H.; Rand, Kasper D.; Østergaard, Henrik; Persson, Egon
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /04/2007 EN
Relevância na Pesquisa
45.97%
Coagulation factor VIIa (FVIIa) requires tissue factor (TF) to attain full catalytic competency and to initiate blood coagulation. In this study, the mechanism by which TF allosterically activates FVIIa is investigated by a structural dynamics approach that combines molecular dynamics (MD) simulations and hydrogen/deuterium exchange (HX) mass spectrometry on free and TF-bound FVIIa. The differences in conformational dynamics from MD simulations are shown to be confined to regions of FVIIa observed to undergo structural stabilization as judged by HX experiments, especially implicating activation loop 3 (residues 365–374{216–225}) of the so-called activation domain and the 170-loop (residues 313–322{170A–175}) succeeding the TF-binding helix. The latter finding is corroborated by experiments demonstrating rapid deglycosylation of Asn322 in free FVIIa by PNGase F but almost complete protection in the presence of TF or an active-site inhibitor. Based on MD simulations, a key switch of the TF-induced structural changes is identified as the interacting pair Leu305{163} and Phe374{225} in FVIIa, whose mutual conformations are guided by the presence of TF and observed to be closely linked to the structural stability of activation loop 3. Altogether...

An Unstructured Finite Volume Approach for Structural Dynamics in Response to Fluid Motions

Xia, Guohua; Lin, Ching-Long
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /04/2008 EN
Relevância na Pesquisa
46.02%
A new cell-vortex unstructured finite volume method for structural dynamics is assessed for simulations of structural dynamics in response to fluid motions. A robust implicit dual-time stepping method is employed to obtain time accurate solutions. The resulting system of algebraic equations is matrix-free and allows solid elements to include structure thickness, inertia, and structural stresses for accurate predictions of structural responses and stress distributions. The method is coupled with a fluid dynamics solver for fluid-structure interaction, providing a viable alternative to the finite element method for structural dynamics calculations. A mesh sensitivity test indicates that the finite volume method is at least of second-order accuracy. The method is validated by the problem of vortex-induced vibration of an elastic plate with different initial conditions and material properties. The results are in good agreement with existing numerical data and analytical solutions. The method is then applied to simulate a channel flow with an elastic wall. The effects of wall inertia and structural stresses on the fluid flow are investigated.

On the Role of Protein Structural Dynamics in the Catalytic Activity and Thermostability of Serine Protease Subtilisin Carlsberg

Castillo, Miraida Pagán; Solá, Ricardo J.; Griebenow, Kai
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/05/2009 EN
Relevância na Pesquisa
45.99%
The effect of modulating the structural dynamics by incremental glycosylation on enzyme activity and thermostability has thus far only been investigated in detail for the serine protease α-chymotrypsin (for a recent review see Solá et al., Cell. Mol. Life Sci. 2007, 64(16):2133–2152). Herein, we extend this type of study to a structurally unrelated serine protease, specifically, subtilisin Carlsberg. The protease was glycosylated with activated lactose and various lactose-subtilisin conjugates were obtained and characterized. Near UV-CD spectroscopy revealed that the tertiary structure was unaffected by the procedure. H/D exchange FT-IR spectroscopy was performed to assess the structural dynamics of the enzyme. It was found that increasing the level of glycosylation caused a linearly dependent reduction in structural dynamics. This led to an increase in thermostability and a decrease in the catalytic turnover rate for both, acylation and de-acylation step. These data highlight the possibility that a structural dynamics – activity relationship might be a phenomenon generally found in serine proteases.

Enzymatic Activity versus Structural Dynamics: The Case of Acetylcholinesterase Tetramer

Gorfe, Alemayehu A.; Lu, Benzhuo; Yu, Zeyun; McCammon, J. Andrew
Fonte: The Biophysical Society Publicador: The Biophysical Society
Tipo: Artigo de Revista Científica
Publicado em 05/08/2009 EN
Relevância na Pesquisa
45.94%
The function of many proteins, such as enzymes, is modulated by structural fluctuations. This is especially the case in gated diffusion-controlled reactions (where the rates of the initial diffusional encounter and of structural fluctuations determine the overall rate of the reaction) and in oligomeric proteins (where function often requires a coordinated movement of individual subunits). A classic example of a diffusion-controlled biological reaction catalyzed by an oligomeric enzyme is the hydrolysis of synaptic acetylcholine (ACh) by tetrameric acetylcholinesterase (AChEt). Despite decades of efforts, the extent to which enzymatic efficiency of AChEt (or any other enzyme) is modulated by flexibility is not fully determined. This article attempts to determine the correlation between the dynamics of AChEt and the rate of reaction between AChEt and ACh. We employed equilibrium and nonequilibrium electro-diffusion models to compute rate coefficients for an ensemble of structures generated by molecular dynamics simulation. We found that, for the static initial model, the average reaction rate per active site is ∼22–30% slower in the tetramer than in the monomer. However, this effect of tetramerization is modulated by the intersubunit motions in the tetramer such that a complex interplay of steric and electrostatic effects either guides or blocks the substrate into or from each of the four active sites. As a result...

Stabilization of α-Chymotrypsin upon PEGylation Correlates with Reduced Structural Dynamics

Rodríguez-Martínez, José A.; Solá, Ricardo J.; Castillo, Betzaida; Cintrón-Colón, Héctor R.; Rivera-Rivera, Izarys; Barletta, Gabriel; Griebenow, Kai
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 15/12/2008 EN
Relevância na Pesquisa
45.97%
Protein stability remains one of the main factors limiting the realization of the full potential of protein therapeutics. Poly(ethylene glycol) (PEG) conjugation to proteins has evolved into an important tool to overcome instability issues associated with proteins. The observed increase in thermodynamic stability of several proteins upon PEGylation has been hypothesized to arise from reduced protein structural dynamics, although experimental evidence for this hypothesis is currently missing. To test this hypothesis, the model protein α-chymotrypsin (α-CT) was covalently modified with PEGs with molecular weights (MW) of 700, 2000 and 5000 and the degree of modification was systematically varied. The procedure did not cause significant tertiary structure changes. Thermodynamic unfolding experiments revealed that PEGylation increased the thermal transition temperature (Tm) of α-CT by up to 6°C and the free energy of unfolding (ΔGU (25°C)) by up to 5 kcal/mol. The increase in stability was found to be independent of the PEG MW and it leveled off after an average of four PEG molecules were bound to α-CT. Fourier-transformed infrared (FTIR) H/D exchange experiments were conducted to characterize the conformational dynamics of the PEG-conjugates. It was found that the magnitude of thermodynamic stabilization correlates with a reduction in protein structural dynamics and was independent of the PEG MW. Thus...

Structural dynamics of synapses in vivo correlate with functional changes during experience-dependent plasticity in visual cortex

Tropea, Daniela; Majewska, Ania K; Garcia, Rodrigo; Sur, Mriganka
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 18/08/2010 EN
Relevância na Pesquisa
45.94%
The impact of activity on neuronal circuitry is complex, involving both functional and structural changes whose interaction is largely unknown. We have used optical imaging of mouse visual cortex responses and two-photon imaging of superficial layer spines on layer 5 neurons to monitor network function and synaptic structural dynamics in the mouse visual cortex in vivo. Total lack of vision due to dark-rearing from birth dampens visual responses and shifts spine dynamics and morphologies toward an immature state. The effects of vision after dark rearing are strongly dependent on the timing of exposure: over a period of days, functional and structural changes are temporally related such that light stabilizes spines while increasing visually-driven activity. The effects of long-term light exposure can be partially mimicked by experimentally enhancing inhibitory signaling in the darkness. Brief light exposure, however, results in a rapid, transient, NMDA-dependent increase of cortical responses, accompanied by increased dynamics of dendritic spines. These findings indicate that visual experience induces rapid reorganization of cortical circuitry followed by a period of stabilization, and demonstrate a close relationship between dynamic changes at single synapses and cortical network function.

Sequence Evolution Correlates with Structural Dynamics

Liu, Ying; Bahar, Ivet
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.05%
Biochemical activity and core stability are essential properties of proteins, maintained usually by conserved amino acids. Structural dynamics emerged in recent years as another essential aspect of protein functionality. Structural dynamics enable the adaptation of the protein to binding substrates and to undergo allosteric transitions, while maintaining the native fold. Key residues that mediate structural dynamics would thus be expected to be conserved or exhibit coevolutionary patterns at least. Yet, the correlation between sequence evolution and structural dynamics is yet to be established. With recent advances in efficient characterization of structural dynamics, we are now in a position to perform a systematic analysis. In the present study, a set of 34 enzymes representing various folds and functional classes is analyzed using information theory and elastic network models. Our analysis shows that the structural regions distinguished by their coevolution propensity as well as high mobility are predisposed to serve as substrate recognition sites, whereas residues acting as global hinges during collective dynamics are often supported by conserved residues. We propose a mobility scale for different types of amino acids, which tends to vary inversely with amino acid conservation. Our findings suggest the balance between physical adaptability (enabled by structure-encoded motions) and chemical specificity (conferred by correlated amino acid substitutions) underlies the selection of a relatively small set of versatile folds by proteins.

Structural dynamics flexibility informs function and evolution at a proteome scale

Nevin Gerek, Zeynep; Kumar, Sudhir; Banu Ozkan, Sefika
Fonte: Blackwell Publishing Ltd Publicador: Blackwell Publishing Ltd
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.95%
Protein structures are dynamic entities with a myriad of atomic fluctuations, side-chain rotations, and collective domain movements. Although the importance of these dynamics to proper functioning of proteins is emerging in the studies of many protein families, there is a lack of broad evidence for the critical role of protein dynamics in shaping the biological functions of a substantial fraction of residues for a large number of proteins in the human proteome. Here, we propose a novel dynamic flexibility index (dfi) to quantify the dynamic properties of individual residues in any protein and use it to assess the importance of protein dynamics in 100 human proteins. Our analyses involving functionally critical positions, disease-associated and putatively neutral population variations, and the rate of interspecific substitutions per residue produce concordant patterns at a proteome scale. They establish that the preservation of dynamic properties of residues in a protein structure is critical for maintaining the protein/biological function. Therefore, structural dynamics needs to become a major component of the analysis of protein function and evolution. Such analyses will be facilitated by the dfi, which will also enable the integrative use of structural dynamics with evolutionary conservation in genomic medicine as well as functional genomics investigations.

Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes

Kel, Oksana; Tamimi, Amr; Fayer, Michael D.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.93%
Plasma membranes hold a wide variety of proteins and other biomolecules that are essential to cell functions. In addition, membranes are the solvent bath, which is intimately coupled to transmembrane processes. Membranes are frequently modeled using planar phospholipid bilayers and vesicles. However, vesicles are small and have relatively small radii of curvature. Research has shown that the bilayer curvature influences structural and thermodynamic properties, but much less is known about the interior dynamics of model membranes. Here we address ultrafast structural dynamics inside vesicle and planar bilayers using 2D IR vibrational echo experiments. The results show that the interior dynamics depend on the phospholipid chain length and are curvature dependent, with the dynamics becoming faster as the vesicle size decreases.

The pH-Dependent Picosecond Structural Dynamics in the Distal Pocket of Nitrophorin 4 Investigated by 2D IR Spectroscopy

Cheng, Mark; Brookes, Jennifer F.; Montfort, William R.; Khalil, Munira
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.01%
Nitrophorin 4 (NP4) belongs to a family of pH-sensitive, nitric oxide (NO) transporter proteins which undergo a large structural change from a closed to an open conformation at high pH to allow for NO delivery. Measuring the pH-dependent structural dynamics in NP4–NO around the ligand binding site is crucial for developing a mechanistic understanding of NO binding and release. In this study we use coherent two-dimensional infrared (2D IR) spectroscopy to measure picosecond structural dynamics sampled by the nitrosyl stretch in NP4–NO as a function of pH at room temperature. Our results show that both the closed and open conformers of the protein are present at low (pD 5.1) and high (pD 7.9) pH conditions. The closed and open conformers are characterized by two frequencies of the nitrosyl stretching vibration labeled A0 and A1, respectively. Analysis of the 2D IR lineshapes reveals that at pD 5.1, the closed conformer experiences structural fluctuations arising from solvation dynamics on a ∼3 ps timescale. At pD 7.9, both the open and closed conformers exhibit fluctuations on a ∼1 ps timescale. At both pD conditions, the closed conformers maintain a static distribution of structures within the experimental time window of 100 ps. This is in contrast to the open conformer...

Modeling Flexibility of Protein-DNA and Protein-Ligand Complexes using Molecular Dynamics; Modellierung der Flexibilität von Protein-DNA und Protein-Ligand Komplexen mit Hilfe von Molekulardynamischen Simulationen

Fischer, Nina M.
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
EN
Relevância na Pesquisa
45.98%
Molecular dynamics simulations provide valuable insights into the inherent flexibility of biomolecules and complement the static structures obtained from X-ray crystallography. Structural dynamics of proteins and alterations at protein-DNA and protein-ligand binding interfaces can thus be investigated. Regulation of gene expression plays a pivotal role in cellular processes and is modulated by special proteins binding to specific DNA sequences. WRKY proteins represent a large protein family in plants and are involved in the regulation of developmental processes, such as leaf senescence, as well as in the response to abiotic and biotic stress situations. The highly conserved WRKY DNA-binding domain recognizes predominantly the ‘TTGACC’ W-box consensus sequence. Since all WRKY proteins prefer this DNA sequence motif, it remains unclear so far how stimulus-specific responses are mediated. The W-box sequence might be more degenerate and yet undetected differences at the protein-DNA binding interface might exist. With molecular modeling and molecular dynamics simulations we constructed a first three-dimensional WRKY-DNA complex at atomic detail. Our modeling approach facilitates the investigation of structural differences and similarities of WRKY DNA-binding domains in complex with DNA while accounting for flexibility. Complexes of N- and C-terminal DNA-binding domains of AtWRKY33 with DNA and in silico binding free energy predictions gave a first indication that the N-terminal domain interacts with DNA in a similar way as the C-terminal domain. Additionally...

Application of weight functions in nonlinear analysis of structural dynamics problems

Ghassemieh, M.; Gholampour, A.A.; Massah, S.R.
Fonte: World Scientific Publishing Publicador: World Scientific Publishing
Tipo: Artigo de Revista Científica
Publicado em //2015 EN
Relevância na Pesquisa
65.94%
This paper presents a weighted residual method with several weight functions for solving differential equation of motion in nonlinear structural dynamics problems. Order of variation of acceleration is assumed to be quadratic in each time step in which polynomial of displacement would contain five unknown coefficients. Five equations are required for determination of these coefficients in each time step. These equations are obtained from initial conditions, satisfying equation of motions at both ends, and weighted residual integration. In this study, four procedures are considered for weight function to be used in the weighted residual integration as; unit weight function, Petrov–Galerkin's weight function, least square weight function, and collocation weight function. Due to higher order of acceleration in the proposed method, the results indicate better and more accurate responses. Among the tested functions, the unit weighted function method demonstrated to be non-dissipative and its numerical dispersion showed to be clearly less than the common Newmark's linear acceleration method. Also critical time step duration in stability investigation for weighted function procedure showed to be larger than the critical time step duration obtained by other methods used in the nonlinear structural dynamics problems.; M. Ghassemieh...

Enterprise design for dynamic complexity : architecting & engineering organizations using system & structural dynamics

Piepenbrock, Theodore F. (Theodore Frederick), 1965-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 2 v. (341 leaves); 17580464 bytes; 17605655 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
45.93%
As the business world is neither linear nor static, the mastery of its "chaotic" nonlinear dynamics lies at the heart of finding high-leverage policies that return uncommon benefits for marginal costs. Today's global enterprises are dynamically complex socio-technical systems where cause and effect of management's strategies and policies are distant in space and time. Spatial complexity recognizes that correctly defining the limits of the extended enterprise is essential in maximizing shareholder value via stakeholder management. Temporal complexity recognizes that policies, decisions, structure and delays are interrelated to influence growth and stability. An enterprise's long-term success therefore is a function of management's ability to control this "dynamic complexity". The goal of this thesis is to develop management insights into "enterprise design", i.e. to create more successful management policies and organizational structures. Enterprise design can be decomposed into the science and art, or engineering and architecting. Using the heretofore-separate academic fields of system dynamics and structural dynamics, an attempt is made to define the scientific "laws" of enterprise physics that will then be used to construct non-obvious...

A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu

Mercier, Evan; Girodat, Dylan; Wieden, Hans-Joachim
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Publicado em 08/01/2015 EN
Relevância na Pesquisa
45.93%
The phosphate-binding loop (P-loop) is a conserved sequence motif found in mononucleotide-binding proteins. Little is known about the structural dynamics of this region and its contribution to the observed nucleotide binding properties. Understanding the underlying design principles is of great interest for biomolecular engineering applications. We have used rapid-kinetics measurements in vitro and molecular dynamics (MD) simulations in silico to investigate the relationship between GTP-binding properties and P-loop structural dynamics in the universally conserved Elongation Factor (EF) Tu. Analysis of wild type EF-Tu and variants with substitutions at positions in or adjacent to the P-loop revealed a correlation between P-loop flexibility and the entropy of activation for GTP dissociation. The same variants demonstrate more backbone flexibility in two N-terminal amino acids of the P-loop during force-induced EF-Tu·GTP dissociation in Steered Molecular Dynamics simulations. Amino acids Gly18 and His19 are involved in stabilizing the P-loop backbone via interactions with the adjacent helix C. We propose that these P-loop/helix C interactions function as a conserved P-loop anchoring module and identify the presence of P-loop anchors within several GTPases and ATPases suggesting their evolutionary conservation.

Structural Dynamics of Free Proteins in Diffraction

Lin, Milo M.; Shorokhov, Dmitry; Zewail, Ahmed H.
Fonte: American Chemical Society Publicador: American Chemical Society
Tipo: Article; PeerReviewed Formato: application/pdf
Publicado em 26/10/2011
Relevância na Pesquisa
45.94%
Among the macromolecular patterns of biological significance, right-handed α-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix-coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an α-helical protein segment thymosin β_9 (Tβ_9), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix-coil transitions in Tβ_9, in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (α-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly...

Structural dynamics and transient electric-field effects in ultrafast electron diffraction from surfaces

Schäfer, Sascha; Liang, Wenxi; Zewail, Ahmed H.
Fonte: Elsevier Publicador: Elsevier
Tipo: Article; PeerReviewed Formato: application/pdf
Publicado em 17/06/2010
Relevância na Pesquisa
45.94%
Ultrafast electron microscopy and diffraction provide direct visualization of structural dynamics with atomic scale resolution. In surface diffraction studies, it may have been assumed that the generation of transient electric fields could mask some features of structural dynamics. Here, we show that such an effect is irrelevant when ultrafast electron microscopy is invoked. It is also demonstrated that for the diffraction investigation of surfaces at grazing angles it is straightforward to observe the structural dynamics provided that simple controls are made for diffraction dependencies on order and intensity, and a comparison with the behavior of the undiffracted beam.

Nonlinear structural dynamics analysis using weighted residual integration

Gholampour, A.A.; Ghassemieh, M.
Fonte: Taylor & Francis Publicador: Taylor & Francis
Tipo: Artigo de Revista Científica
Publicado em //2013 EN
Relevância na Pesquisa
65.88%
A new time integration method is proposed for solving a differential equation of motion of structural dynamics problems with nonlinear stiffness. In this method, it is assumed that order of variation of acceleration is quadratic in each time step and, therefore, variation of displacement in each time step is a fourth-order polynomial that has five coefficients. Other than implementing initial conditions and satisfying equation of motions at both ends, weighted residual integral is also used in order to evaluate the unknown coefficients. By increasing order of acceleration, more terms of Taylor series are used, which were expected to have better responses than the other classical methods. The proposed method is non-dissipative and its numerical dispersion showed to be clearly less than the other methods. By studying stability of the method, it reveals that critical time step duration for the proposed method can be larger than the critical time step duration obtained from other classical methods; also, computational time for analysis with critical time step duration for the proposed method becomes less in comparison with linear acceleration and central difference methods. The order of accuracy of the proposed method is four, which showed to be very accurate in almost all practical problems.; A. A. Gholampour...