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Dynamic systems theory

Bartosz Błasiak, Casey H Londergan, Lauren J Webb, Minhaeng Cho
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies...
March 27, 2017: Accounts of Chemical Research
J Ambjørn, J Gizbert-Studnicki, A Görlich, J Jurkiewicz, N Klitgaard, R Loll
The approach of Causal Dynamical Triangulations (CDT), a candidate theory of nonperturbative quantum gravity in 4D, turns out to have a rich phase structure. We investigate the recently discovered bifurcation phase [Formula: see text] and relate some of its characteristics to the presence of singular vertices of very high order. The transition lines separating this phase from the "time-collapsed" B-phase and the de Sitter phase [Formula: see text] are of great interest when searching for physical scaling limits...
2017: European Physical Journal. C, Particles and Fields
Joana Cabral, Morten Kringelbach, Gustavo Deco
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...
March 23, 2017: NeuroImage
J Ma, D A Pesin
We develop an effective medium theory for electromagnetic wave propagation through gapless nonuniform systems with a dynamic chiral magnetic effect. The theory allows us to calculate macroscopic-disorder-induced corrections to the values of optical, as well as chiral magnetic conductivities. In particular, we show that spatial fluctuations of the optical conductivity induce corrections to the effective value of the chiral magnetic conductivity. The absolute value of the effect varies strongly depending on the system parameters, but yields the leading frequency dependence of the polarization rotation and circular dichroism signals...
March 10, 2017: Physical Review Letters
Zhi Yan, Liying Jiang
Piezoelectric nanomaterials (PNs) are attractive for applications including sensing, actuating, energy harvesting, among others in nano-electro-mechanical-systems (NEMS) because of their excellent electromechanical coupling, mechanical and physical properties. However, the properties of PNs do not coincide with their bulk counterparts and depend on the particular size. A large amount of efforts have been devoted to studying the size-dependent properties of PNs by using experimental characterization, atomistic simulation and continuum mechanics modeling with the consideration of the scale features of the nanomaterials...
January 26, 2017: Nanomaterials
Momir Mališ, Nađa Došlić
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory...
March 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Mari-K H Winkler, Pieter Boets, Birk Hahne, Peter Goethals, Eveline I P Volcke
The conditions present in both in vitro and in vivo ecosystems determine the microbial population harbouring it. One commonly accepted theory is that a species with a high substrate affinity and low growth rate (k-strategist) will win the competition against a second species with a lower substrate affinity and higher growth rate (r-strategist) if both species are subjected to low substrate concentrations. In this study two nitrite oxidizing bacteria (NOB), Nitrospira defluvii (k-strategist) and Nitrobacter vulgaris (r-strategist), were cultivated in a continuous reactor systems...
2017: PloS One
Mátyás Herein, Gábor Drótos, Tímea Haszpra, János Márfy, Tamás Tél
Teleconnections are striking features of the Earth climate system which appear as statistically correlated climate-related patterns between remote geographical regions of the globe. In a changing climate, however, the strength of teleconnections might change, and an appropriate characterization of these correlations and their change (more appropriate than detrending the time series) is lacking in the literature. Here we present a novel approach, based on the theory of snapshot attractors, corresponding in our context to studying parallel climate realizations...
March 23, 2017: Scientific Reports
Bobo Cao, Jiuyao Du, Ziping Cao, Haitao Sun, Xuejun Sun, Hui Fu
To explore sustainable catalysts with innovative mechanisms, the alkylation mechanism of o-xylene with styrene was studied using DFT method in AlCl3-ionic liquid catalytic system. The reaction pathway was consisted of CC coupling and a hydrogen shift, in which two transition states were found and further discussed. The reactive energy catalyzed by superelectrophilic AlCl2(+) (12.6kcal/mol) was distinctly lower than AlCl3 (43.0kcal/mol), which was determined as the rate-determining step. Mulliken charge along IRC gave a comprehensive understanding of charge distribution and electron transfer in dynamic progress...
March 6, 2017: Journal of Molecular Graphics & Modelling
Frank Noé, Cecilia Clementi
Collective variables are an important concept to study high-dimensional dynamical systems, such as molecular dynamics of macromolecules, liquids, or polymers, in particular to define relevant metastable states and state-transition or phase-transition. Over the past decade, a rigorous mathematical theory has been formulated to define optimal collective variables to characterize slow dynamical processes. Here we review recent developments, including a variational principle to find optimal approximations to slow collective variables from simulation data, and algorithms such as the time-lagged independent component analysis...
March 16, 2017: Current Opinion in Structural Biology
Mark A Elliott, Naomi du Bois
From the point of view of the cognitive dynamicist the organization of brain circuitry into assemblies defined by their synchrony at particular (and precise) oscillation frequencies is important for the correct correlation of all independent cortical responses to the different aspects of a given complex thought or object. From the point of view of anyone operating complex mechanical systems, i.e., those comprising independent components that are required to interact precisely in time, it follows that the precise timing of such a system is essential - not only essential but measurable, and scalable...
2017: Frontiers in Psychology
David A Peterson, Terrence J Sejnowski
Blepharospasm (sometimes called "benign essential blepharospasm," BEB) is one of the most common focal dystonias. It involves involuntary eyelid spasms, eye closure, and increased blinking. Despite the success of botulinum toxin injections and, in some cases, pharmacologic or surgical interventions, BEB treatments are not completely efficacious and only symptomatic. We could develop principled strategies for preventing and reversing the disease if we knew the pathogenesis of primary BEB. The objective of this study was to develop a conceptual framework and dynamic circuit hypothesis for the pathogenesis of BEB...
2017: Frontiers in Computational Neuroscience
Soohaeng Yoo Willow, Sotiris S Xantheas
The effect of the Hofmeister anions on the precipitation of proteins is often discussed using liquid-vapor coexisting systems with the assumption that the liquid-vapor interface mimics the liquid-protein interface. Solvated proteins, however, have both hydrophobic and hydrophilic regions on their surfaces rather than just a pure hydrophobic one. Using a solvated parallel β-sheet layer consisting of both hydrophobic and positively charged hydrophilic surfaces, we investigated the adsorption of kosmotropic (SO4(2-)) and chaotropic (ClO4(-)) anions towards protein's hydrophobic and hydrophilic surfaces via Born-Oppenheimer molecular dynamics simulations using the BLYP density functional theory...
March 21, 2017: Journal of Physical Chemistry Letters
Riccardo Spezia, Emilio Martínez-Nuñez, Saulo Vazquez, William L Hase
In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
David R Glowacki, W J Rodgers, Robin Shannon, Struan H Robertson, Jeremy N Harvey
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Brooklyn A Noble, C Mathew Mate, Bart Raeymaekers
Ultrathin liquid films play a critical role in numerous engineering applications. Although crucial to the design and application of ultrathin liquid films, the physical mechanisms that govern spreading on the molecular scale are not well-understood, and disagreement among experiments, simulations, and theory remains. We use molecular dynamics simulations to quantify the speed at which the edge of a polymer droplet advances on a flat substrate as a function of various environmental and design parameters. We explain the physical mechanisms that drive and inhibit spreading, identify different spreading regimes, and clarify transitions between spreading regimes...
March 27, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Coralie Pasquier, Mario Vazdar, Jan Forsman, Pavel Jungwirth, Mikael Lund
The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom Molecular Dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) over-charge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction...
March 20, 2017: Journal of Physical Chemistry. B
Sunil Nath
Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis...
March 8, 2017: Biophysical Chemistry
Yihong Wang, Rubin Wang, Xuying Xu
Electrical activity is the foundation of the neural system. Coding theories that describe neural electrical activity by the roles of action potential timing or frequency have been thoroughly studied. However, an alternative method to study coding questions is the energy method, which is more global and economical. In this study, we clearly defined and calculated neural energy supply and consumption based on the Hodgkin-Huxley model, during firing action potentials and subthreshold activities using ion-counting and power-integral model...
2017: Neural Plasticity
Carla H Geveke, Henderien W Steenbeek, Jeannette M Doornenbal, Paul L C Van Geert
In order for out-of-school science activities that take place during school hours but outside the school context to be successful, instructors must have sufficient pedagogical content knowledge (PCK) to guarantee high-quality teaching and learning. We argue that PCK is a quality of the instructor-pupil system that is constructed in real-time interaction. When PCK is evident in real-time interaction, we define it as Expressed Pedagogical Content Knowledge (EPCK). The aim of this study is to empirically explore whether EPCK shows a systematic pattern of variation, and if so whether the pattern occurs in recurrent and temporary stable attractor states as predicted in the complex dynamic systems theory...
2017: Frontiers in Psychology
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