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Dynamic systems theory

Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
Mangesh I Chaudhari, Jijeesh R Nair, Lawrence R Pratt, Fernando A Soto, Perla B Balbuena, Susan Rempe
Lithium ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) are studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to as- sess non-polarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) is adapted to take advantage of four-fold occupancy of the near-neighbor solvation structure observed in simulations, and used to calculate solvation free energies...
October 21, 2016: Journal of Chemical Theory and Computation
Erfan Dashtimoghadam, Ghasem Bahlakeh, Hamed Salimi-Kenari, Mohammad Mahdi Hasani-Sadrabadi, Hamid Mirzadeh, Bo Nyström
The temperature-induced gelation of chitosan/glycerophosphate (Chs/GP) systems through physical interactions has shown great potential for various biomedical applications. In the present work, hydroxyethyl cellulose (HEC) was added to the thermosensitive Chs/GP solution to improve the mechanical strength and gel properties of the incipient Chs/HEC/GP gel in comparison with the Chs/GP hydrogel at body temperature. The physical features of the macromolecular complexes formed by the synergistic interaction between chitosan and hydroxyethyl cellulose in the presence of β-glycerophosphate disodium salt solution have been studied essentially from a rheological point of view...
October 21, 2016: Biomacromolecules
Zhi-Hao Cui, Feng Wu, Hong Jiang
The relative stability of TiO2 in the rutile and anatase structure is wrongly described by density functional theory in various local, semilocal, or even hybrid functional approximations. In this work, we have found that by considering high-order correlations in the adiabatic connection fluctuation-dissipation theory with the random phase approximation (ACFDT-RPA), rutile is correctly predicted to be more stable than anatase, which can be physically attributed to different characters in the electronic band structure of rutile and anatase, including, in particular, that rutile has a smaller band gap than anatase...
October 20, 2016: Physical Chemistry Chemical Physics: PCCP
Jeremy B Yoder
Decades of research on the evolution of mutualism has generated a wealth of possible ways whereby mutually beneficial interactions between species persist in spite of the apparent advantages to individuals that accept the benefits of mutualism without reciprocating - but identifying how any particular empirical system is stabilized against cheating remains challenging. Different hypothesized models of mutualism stability predict different forms of coevolutionary selection, and emerging high-throughput sequencing methods allow examination of the selective histories of mutualism genes and, thereby, the form of selection acting on those genes...
October 18, 2016: American Journal of Botany
Pablo M Piaggi, Omar Valsson, Michele Parrinello
We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations. Therefore we use a recently developed enhanced sampling method [Valsson and Parrinello, Phys. Rev. Lett.113, 090601 (2014)] based on the variational determination of a bias potential. We differ from previous applications of this method in that the bias is constructed on the basis of the physical model provided by the classical theory of nucleation...
October 18, 2016: Faraday Discussions
Qishui Zhong, Fuli Zhong, Jun Cheng, Hui Li, Shouming Zhong
This paper presents a state of charge (SOC) estimation method based on fractional order sliding mode observer (SMO) for lithium-ion batteries. A fractional order RC equivalent circuit model (FORCECM) is firstly constructed to describe the charging and discharging dynamic characteristics of the battery. Then, based on the differential equations of the FORCECM, fractional order SMOs for SOC, polarization voltage and terminal voltage estimation are designed. After that, convergence of the proposed observers is analyzed by Lyapunov's stability theory method...
October 14, 2016: ISA Transactions
David Williams-Young, Joshua J Goings, Xiaosong Li
Solutions of the real-time time-dependent density functional theory (RT-TDDFT) equations provide an affordable route to understanding the electronic dynamics that underpins many spectroscopic techniques. From the solutions of the RT-TDDFT equations it is possible to extract optical absorption and circular dichroism spectra, as well as descriptions of charge transfer and charge transport dynamics. In order to apply RT-TDDFT to increasingly large systems, it is necessary to develop methods to overcome computational bottlenecks...
October 17, 2016: Journal of Chemical Theory and Computation
Marko Melander, Elvar Örn Jónsson, Jens Jørgen Mortensen, Tejs Vegge, Juan María García Lastra
Combining constrained density function theory (cDFT) with Marcus theory is an efficient and promising way to address charge transfer reactions. Here, we present a general and robust implementation of cDFT within the projector augmented wave (PAW) framework. PAW pseudopotentials offer a reliable frozen-core electron description across the whole periodic table, with good transferability, as well as facilitate the extraction of all-electron quantities. The present implementation is applicable to two different wave function representations -- atomic centred basis sets (LCAO) and the finite-difference (FD) approximation utilizing real-space grids...
October 17, 2016: Journal of Chemical Theory and Computation
Guanglei Wang, Ying-Cheng Lai, Celso Grebogi
Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories...
October 17, 2016: Scientific Reports
Koushik Viswanathan, Narayan K Sundaram, Srinivasan Chandrasekar
Stick-slip in sliding of soft adhesive surfaces has long been associated with the propagation of Schallamach waves, a type of slow surface wave. Recently it was demonstrated using in situ experiments that two other kinds of slow waves-separation pulses and slip pulses-also mediate stick-slip (Viswanathan et al., Soft Matter, 2016, 12, 5265-5275). While separation pulses, like Schallamach waves, involve local interface detachment, slip pulses are moving stress fronts with no detachment. Here, we present a theoretical analysis of the propagation of these three waves in a linear elastodynamics framework...
October 17, 2016: Soft Matter
Xuewen Tao, Fuqiang Liu, Zhiping Bai, Dongyang Wei, Xiaopeng Zhang, Junfei Wang, Jie Gao, Xiaowen Sun, Baohua Li, Chenghui Li, Aimin Li
An efficient and profitable separation process was proposed to prepare 5N (the purity of the metal solution reaches 99.999%) high-purity nickel from 3N nickel-solutions using Purolite S984. The adsorption performance of this superior resin, especially its selectivity for metal ions, was explored quantitatively. The maximum adsorption capacity for copper was 2.286mmol/g calculated by the Langmuir model, which was twice as large as that for nickel. In the binary systems, the adsorption capacity for nickel was decreased by 45%, indicating direct competition for the active sites...
October 2016: Journal of Environmental Sciences (China)
Sylvain Billiard, Pierre Collet, Régis Ferrière, Sylvie Méléard, Viet Chi Tran
Horizontal transfer (HT) of heritable information or 'traits' (carried by genetic elements, plasmids, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is scant. We present a modeling framework for the dynamics of two populations that compete for resources and horizontally exchange (transfer) an otherwise vertically inherited trait. Competition infuences individual demographics, thereby affecting population size, which feeds back on the dynamics of transfer...
October 11, 2016: Journal of Theoretical Biology
Douglas McLelland, Rufin VanRullen
Several theories have been advanced to explain how cross-frequency coupling, the interaction of neuronal oscillations at different frequencies, could enable item multiplexing in neural systems. The communication-through-coherence theory proposes that phase-matching of gamma oscillations between areas enables selective processing of a single item at a time, and a later refinement of the theory includes a theta-frequency oscillation that provides a periodic reset of the system. Alternatively, the theta-gamma neural code theory proposes that a sequence of items is processed, one per gamma cycle, and that this sequence is repeated or updated across theta cycles...
October 2016: PLoS Computational Biology
Masaharu Isobe, Aaron S Keys, David Chandler, Juan P Garrahan
We numerically investigate the applicability of dynamic facilitation (DF) theory for glass-forming binary hard disk systems where supercompression is controlled by pressure. By using novel efficient algorithms for hard disks, we are able to generate equilibrium supercompressed states in an additive nonequimolar binary mixture, where microcrystallization and size segregation do not emerge at high average packing fractions. Above an onset pressure where collective heterogeneous relaxation sets in, we find that relaxation times are well described by a "parabolic law" with pressure...
September 30, 2016: Physical Review Letters
C Wan, M Scala, G W Morley, Atm A Rahman, H Ulbricht, J Bateman, P F Barker, S Bose, M S Kim
We propose an interferometric scheme based on an untrapped nano-object subjected to gravity. The motion of the center of mass (c.m.) of the free object is coupled to its internal spin system magnetically, and a free flight scheme is developed based on coherent spin control. The wave packet of the test object, under a spin-dependent force, may then be delocalized to a macroscopic scale. A gravity induced dynamical phase (accrued solely on the spin state, and measured through a Ramsey scheme) is used to reveal the above spatially delocalized superposition of the spin-nano-object composite system that arises during our scheme...
September 30, 2016: Physical Review Letters
Timur V Tscherbul, Paul Brumer, Alexei A Buchachenko
We present accurate ab initio and quantum scattering calculations on a prototypical hybrid ion-atom system Yb^{+}-Rb, recently suggested as a promising candidate for the experimental study of open quantum systems, quantum information processing, and quantum simulation. We identify the second-order spin-orbit (SO) interaction as the dominant source of hyperfine relaxation in cold Yb^{+}-Rb collisions. Our results are in good agreement with recent experimental observations [L. Ratschbacher et al., Phys. Rev...
September 30, 2016: Physical Review Letters
Eugene Stephane Mananga, Bingwen Hu
The importance of the average Hamiltonian theory and its antecedent the Magnus expansion are discussed. The investigation of its convergence in different situations is very important. In this paper, we introduced a well-established approach to minimize the zeroth order average Hamiltonian for modified composite pulse sequence in quadrupolar spectroscopy of spin-1. We designed two modified composite pulse sequences constructed by modifying the timing sequence in the original composite pulse sequences17. We tested various configurations of times associated with the free evolution of spin system in the modified composite pulses...
October 14, 2016: Journal of Physical Chemistry. A
Guoxing Wen, C L Philip Chen, Yan-Jun Liu, Zhi Liu
Compared with the existing neural network (NN) or fuzzy logic system (FLS) based adaptive consensus methods, the proposed approach can greatly alleviate the computation burden because it needs only to update a few adaptive parameters online. In the multiagent agreement control, the system uncertainties derive from the unknown nonlinear dynamics are counteracted by employing the adaptive NNs; the state delays are compensated by designing a Lyapunov-Krasovskii functional. Finally, based on Lyapunov stability theory, it is demonstrated that the proposed consensus scheme can steer a multiagent system synchronizing to the predefined reference signals...
October 11, 2016: IEEE Transactions on Cybernetics
Bethany Lusch, Pedro D Maia, J Nathan Kutz
Determining the interactions and causal relationships between nodes in an unknown networked dynamical system from measurement data alone is a challenging, contemporary task across the physical, biological, and engineering sciences. Statistical methods, such as the increasingly popular Granger causality, are being broadly applied for data-driven discovery of connectivity in fields from economics to neuroscience. A common version of the algorithm is called pairwise-conditional Granger causality, which we systematically test on data generated from a nonlinear model with known causal network structure...
September 2016: Physical Review. E
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