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Systems Dynamics

Kelsey A Herrmann, Heather T Broihier
Although retrograde neurotrophin signaling has provided an immensely influential paradigm for understanding growth factor signaling in the nervous system, recent studies indicate that growth factors also signal via cell-autonomous, or autocrine, mechanisms. Autocrine signals have been discovered in many neuronal contexts, providing insights into their regulation and function. The growing realization of the importance of cell-autonomous signaling stems from advances in both conditional genetic approaches and in sophisticated analyses of growth factor dynamics, which combine to enable rigorous in vivo dissection of signaling pathways...
March 13, 2018: Current Opinion in Neurobiology
Christine Prouty, Shima Mohebbi, Qiong Zhang
Given the increasing vulnerability of communities to the negative impacts of untreated wastewater, resource recovery (RR) systems provide a paradigm shift away from a traditional approach of waste separation and treatment towards a productive recovery of water, energy and nutrients. The aim of this research is to understand the relationships between factors that influence the adoption and sustainability of wastewater-based RR systems to inform technology implementation strategies. The study presents a theory-informed, community-influenced system dynamics (SD) model to provide decision-makers with an adaptable tool that simulates system-level responses to the strategies that are developed for the coastal town of Placencia, Belize...
March 7, 2018: Water Research
María Victoria Repetto, Matthew J Winters, Alan Bush, Wolfgang Reiter, David Maria Hollenstein, Gustav Ammerer, Peter M Pryciak, Alejandro Colman-Lerner
We report an unanticipated system of joint regulation by cyclin-dependent kinase (CDK) and mitogen-activated protein kinase (MAPK), involving collaborative multi-site phosphorylation of a single substrate. In budding yeast, the protein Ste5 controls signaling through a G1 arrest pathway. Upon cell-cycle entry, CDK inhibits Ste5 via multiple phosphorylation sites, disrupting its membrane association. Using quantitative time-lapse microscopy, we examined Ste5 membrane recruitment dynamics at different cell-cycle stages...
March 15, 2018: Molecular Cell
Shushan He, Lutz Maibaum
Understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step towards unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. We use coarse-grained molecular dynamics simulations to study the composition phase diagram of a quaternary mixture of phospholipids and cholesterol. This mixture is known to exhibit both uniform and coexisting phases. We compare and combine different statistical measures of membrane structure to identify the onset of phase coexistence in composition space...
March 16, 2018: Journal of Physical Chemistry. B
Qiang Zhang, Tianyuan Xin, Xiaoke Lu, Yuexia Wang
We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method...
March 16, 2018: Materials
Jessica H Hill, Claudia Solt, Michelle T Foster
Obesity and associated metabolic co-morbidities are a worldwide public health problem. Negative health outcomes associated with obesity, however, do not arise from excessive adiposity alone. Rather, deleterious outcomes of adipose tissue accumulation are a result of how adipocytes are distributed to individual regions in the body. Due to our increased understanding of the dynamic relationship that exists between specific adipose depots and disease risk, an accurate characterization of total body adiposity as well as location is required to properly evaluate a population's disease risk...
March 16, 2018: Hormone Molecular Biology and Clinical Investigation
J-F Rupprecht, A Singh Vishen, G V Shivashankar, M Rao, J Prost
We investigate the effect of stress fluctuations on the stochastic dynamics of an inclusion embedded in a viscous gel. We show that, in nonequilibrium systems, stress fluctuations give rise to an effective attraction towards the boundaries of the confining domain, which is reminiscent of an active Casimir effect. We apply this generic result to the dynamics of deformations of the cell nucleus, and we demonstrate the appearance of a fluctuation maximum at a critical level of activity, in agreement with recent experiments [E...
March 2, 2018: Physical Review Letters
Yongxi Ou, D C Ralph, R A Buhrman
Robust spin Hall effects (SHE) have recently been observed in nonmagnetic heavy metal systems with strong spin-orbit interactions. These SHE are either attributed to an intrinsic band-structure effect or to extrinsic spin-dependent scattering from impurities, namely, side jump or skew scattering. Here we report on an extraordinarily strong spin Hall effect, attributable to spin fluctuations, in ferromagnetic Fe_{x}Pt_{1-x} alloys near their Curie point, tunable with x. This results in a dampinglike spin-orbit torque being exerted on an adjacent ferromagnetic layer that is strongly temperature dependent in this transition region, with a peak value that indicates a lower bound 0...
March 2, 2018: Physical Review Letters
Thomas Lilienkamp, Ulrich Parlitz
Transient chaos in spatially extended systems can be characterized by the length of the transient phase, which typically grows quickly with the system size (supertransients). For a large class of these systems, the chaotic phase terminates abruptly, without any obvious precursors in commonly used observables. Here we investigate transient spatiotemporal chaos in two different models of this class. By probing the state space using perturbed trajectories we show the existence of a "terminal transient phase," which occurs prior to the abrupt collapse of chaotic dynamics...
March 2, 2018: Physical Review Letters
Chang-Hwan Yi, Julius Kullig, Jan Wiersig
One of the interesting features of open quantum and wave systems is the non-Hermitian degeneracy called an exceptional point, where not only energy levels but also the corresponding eigenstates coalesce. We demonstrate that such a degeneracy can appear in optical microdisk cavities by deforming the boundary extremely weakly. This surprising finding is explained by a semiclassical theory of dynamical tunneling. It is shown that the exceptional points come in nearly degenerated pairs, originating from the different symmetry classes of modes...
March 2, 2018: Physical Review Letters
Diego Jaramillo-Cano, Maud Formanek, Christos N Likos, Manuel Camargo
Star block-copolymers (SBCs) have been demonstrated to constitute self-assembling building blocks with specific softness, functionalization, shape and flexibility. In this work we study the behaviour of an isolated SBC under shear flow by means of particle-based multi-scale simulations. We systematically analyse the conformational properties of low-functionality stars as well as the formation of attractive patches on their corona as a function of the shear rate. We cover a wide range of system parameters, including functionality, amphiphilicity and solvent quality...
March 16, 2018: Journal of Physical Chemistry. B
Charles M Luft, Elango Munusamy, Jeanne E Pemberton, Steven D Schwartz
A detailed molecular dynamics simulation study is presented on the behavior of aggre- gates composed of the nonionic monorhamnolipid α-rhamnopyranosyl-β-hydroxydecanoyl- β -hydroxydecanoate (Rha-C10-C10) and decane in bulk water. A graph theoretical approach was utilized to characterize the size and composition of the many aggregates generated in our simulations. Overall we observe that the formation of oil in Rha-C10-C10 aggregates is a fa- vorable process. Detailed analysis on the surfactant/oil aggregate shows that larger aggregates are stable...
March 16, 2018: Journal of Physical Chemistry. B
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Lesley W Chan, Daniel E Morse, Michael J Gordon
Near- and sub-wavelength photonic structures are used by numerous organisms (e.g., insects, cephalopods, fish, birds) to create vivid and often dynamically-tunable colors, as well as create, manipulate, or capture light for vision, communication, crypsis, photosynthesis, and defense. This review introduces the physics of moth eye (ME)-like, biomimetic nanostructures and discusses their application to reduce optical losses and improve efficiency of various optoelectronic devices, including photodetectors, photovoltaics, imagers, and light emitting diodes...
March 16, 2018: Bioinspiration & Biomimetics
Xiaodi Niu, Yawen Gao, Yiding Yu, Yanan Yang, Guizhen Wang, Lin Sun, Hongsu Wang
Previous studies found that the activity of Sortase A, a bacterial surface protein from Staphylococcus aureus, was inhibited by curcumin and its analogues. To explore this inhibitory mechanism, Sortase A and its inhibitors in complex systems were studied by molecular docking, molecular modelling, binding energy decomposition calculation, and steered molecular dynamics simulations. Energy decomposition analysis indicated that PRO-163, LEU-169, GLN-172, ILE-182, and ILE-199 are key residues in Sortase A-inhibitor complexes...
March 16, 2018: Journal of Biomolecular Structure & Dynamics
Ayori Mitsutake, Hiroshi Takano
Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special hardware. However, it is necessary to derive the important factors contributing to structural change or function from the complicated movements of biopolymers obtained from long simulations. Although some analysis methods for protein systems have been developed using increasing simulation times, many of these methods are static in nature (i...
March 15, 2018: Biophysical Reviews
Vivek Murthy, Janna Minehart, Daniel H Sterman
Modern cancer immunotherapies represent a major shift in paradigm with respect to how we understand innate and adaptive responses to malignancy. Successful tumors co-opt normal immunosurveillance mechanisms by potent interactions between the tumor and local draining lymph nodes. Tumor cells mediate a complex and dynamic immunoediting procedure that results in increased vascular efflux into the draining lymphatics, an immunosuppressive microenvironment rich in regulatory T-lymphocytes, dysfunctional antigen presentation, and downregulation of normal effector lymphocyte responses...
December 1, 2017: Journal of the National Cancer Institute
Jeon Hyeong Lee, Myoung Hee Lee
[Purpose] This study was performed to analyze the influence of smartphone multitasking on gait and dynamic balance. [Subjects and Methods] The subjects were 19 male and 20 female university students. There were 4 types of gait tasks: General Gait (walking without a task), Task Gait 1 (walking while writing a message), Task Gait 2 (walking while writing a message and listening to music), Task Gait 3 (walking while writing a message and having a conversation). To exclude the learning effect, the order of tasks was randomized...
February 2018: Journal of Physical Therapy Science
Junjie Zhao, Berc Kalanyan, Heather F Barton, Brent A Sperling, Gregory N Parsons
In situ chemical measurements of solution/surface reactions during metal-organic framework (MOF) thin film growth can provide valuable information about the mechanistic and kinetic aspects of key reaction steps, and allow control over crystal quality and material properties. Here, we report a new approach to study the growth of MOF thin films in a flow cell using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Real-time spectra recorded during continuous flow synthesis were used to investigate the mechanism and kinetics that govern the formation of (Zn, Cu) hydroxy double salts (HDSs) from ZnO thin films and the subsequent conversion of HDS to HKUST-1...
October 24, 2017: Chemistry of Materials: a Publication of the American Chemical Society
Guoqi Li, Lei Deng, Gaoxi Xiao, Pei Tang, Changyun Wen, Wuhua Hu, Jing Pei, Luping Shi, H Eugene Stanley
Complex networks characterize the nature of internal/external interactions in real-world systems including social, economic, biological, ecological, and technological networks. Two issues keep as obstacles to fulfilling control of large-scale networks: structural controllability which describes the ability to guide a dynamical system from any initial state to any desired final state in finite time, with a suitable choice of inputs; and optimal control, which is a typical control approach to minimize the cost for driving the network to a predefined state with a given number of control inputs...
March 15, 2018: Scientific Reports
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