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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
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
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
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
Felista L Tansi, Ronny Rüger, Ansgar M Kollmeier, Markus Rabenhold, Frank Steiniger, Roland E Kontermann, Ulf K Teichgraeber, Alfred Fahr, Ingrid Hilger
BACKGROUND: Endoglin (CD105) is overexpressed on tumor cells and tumor vasculatures, making it a potential target for diagnostic imaging and therapy of different neoplasms. Therefore, studies on nanocarrier systems designed for endoglin-directed diagnostic and drug delivery purposes would expose the feasibility of targeting endoglin with therapeutics. METHODS: Liposomes carrying high concentrations of a near-infrared fluorescent dye in the aqueous interior were prepared by the lipid film hydration and extrusion procedure, then conjugated to single chain antibody fragments either selective for murine endoglin (termed mEnd-IL) or directed towards human endoglin (termed hEnd-IL)...
March 12, 2018: Biochimica et Biophysica Acta
Zhen Tian, Jingqi Yuan, Xiang Zhang, Lei Kong, Jingcheng Wang
The coordinated control system (CCS) serves as an important role in load regulation, efficiency optimization and pollutant reduction for coal-fired power plants. The CCS faces with tough challenges, such as the wide-range load variation, various uncertainties and constraints. This paper aims to improve the load tacking ability and robustness for boiler-turbine units under wide-range operation. To capture the key dynamics of the ultra-supercritical boiler-turbine system, a nonlinear control-oriented model is developed based on mechanism analysis and model reduction techniques, which is validated with the history operation data of a real 1000 MW unit...
March 12, 2018: ISA Transactions
Joseph Páez Chávez, Dirk Jungmann, Stefan Siegmund
The paper presents a comprehensive numerical study of mathematical models used to describe complex biological systems in the framework of integrated pest management. Our study considers two specific ecosystems that describe the application of control mechanisms based on pesticides and natural enemies, implemented in an impulsive and periodic manner, due to which the considered models belong to the class of impulsive differential equations. The present work proposes a numerical approach to study such type of models in detail, via the application of path-following (continuation) techniques for nonsmooth dynamical systems, via the novel continuation platform COCO (Dankowicz and Schilder)...
December 2018: Journal of Biological Dynamics
Matthew S Church, Timothy J H Hele, Gregory S Ezra, Nandini Ananth
We extend the Mixed Quantum-Classical Initial Value Representation (MQC-IVR), a semiclassical method for computing real-time correlation functions, to electronically nonadiabatic systems using the Meyer-Miller-Stock-Thoss (MMST) Hamiltonian in order to treat electronic and nuclear degrees of freedom (dofs) within a consistent dynamic framework. We introduce an efficient symplectic integration scheme, the MInt algorithm, for numerical time evolution of the phase space variables and monodromy matrix under the non-separable MMST Hamiltonian...
March 14, 2018: Journal of Chemical Physics
Mariana Rossi, Venkat Kapil, Michele Ceriotti
Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level of control can be achieved for the dynamical properties computed from thermostatted trajectories. We develop quantitative measures of the disturbance induced by the GLE to the Hamiltonian dynamics of a harmonic oscillator, and show that these analytical results accurately predict the behavior of strongly anharmonic systems...
March 14, 2018: Journal of Chemical Physics
Xuecheng Tao, Philip Shushkov, Thomas F Miller
We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation...
March 14, 2018: Journal of Chemical Physics
Xinzijian Liu, Jian Liu
An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties...
March 14, 2018: Journal of Chemical Physics
Igor Poltavsky, Robert A DiStasio, Alexandre Tkatchenko
Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials. In this work, we extend our recently proposed perturbed path-integral (PPI) approach for modeling NQE in molecular systems [I. Poltavsky and A. Tkatchenko, Chem. Sci. 7, 1368 (2016)], which successfully combines the advantages of thermodynamic perturbation theory with path-integral molecular dynamics (PIMD), in a number of important directions...
March 14, 2018: Journal of Chemical Physics
Size Zheng, Katherine S Shing, Muhammad Sahimi
In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis diseases...
March 14, 2018: Journal of Chemical Physics
Yang Xu, Kai Song, Qiang Shi
The hydride transfer reaction catalyzed by dihydrofolate reductase is studied using a recently developed mixed quantum-classical method to investigate the nuclear quantum effects on the reaction. Molecular dynamics simulation is first performed based on a two-state empirical valence bond potential to map the atomistic model to an effective double-well potential coupled to a harmonic bath. In the mixed quantum-classical simulation, the hydride degree of freedom is quantized, and the effective harmonic oscillator modes are treated classically...
March 14, 2018: Journal of Chemical Physics
Junhao Liang, Anwarud Din, Tianshou Zhou
While many physical or chemical systems can be modeled by nonlinear Langevin equations (LEs), dynamical analysis of these systems is challenging in the cases of moderate and strong noise. Here we develop a linear approximation scheme, which can transform an often intractable LE into a linear set of binomial moment equations (BMEs). This scheme provides a feasible way to capture nonlinear behaviors in the sense of probability distribution and is effective even when the noise is moderate or big. Based on BMEs, we further develop a noise reduction technique, which can effectively handle tough cases where traditional small-noise theories are inapplicable...
March 14, 2018: Journal of Chemical Physics
Christian J Burnham, Zdenek Futera, Niall J English
The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model...
March 14, 2018: Journal of Chemical Physics
Sven Karsten, Sergei D Ivanov, Sergey I Bokarev, Oliver Kühn
The framework to approach quasi-classical dynamics in the electronic ground state is well established and is based on the Kubo-transformed time correlation function (TCF), being the most classical-like quantum TCF. Here we discuss whether the choice of the Kubo-transformed TCF as a starting point for simulating vibronic spectra is as unambiguous as it is for vibrational ones. Employing imaginary-time path integral techniques in combination with the interaction representation allowed us to formulate a method for simulating vibronic spectra in the adiabatic regime that takes nuclear quantum effects and dynamics on multiple potential energy surfaces into account...
March 14, 2018: Journal of Chemical Physics
Ciarán L Kelly, George M Taylor, Andrew Hitchcock, Antonio Torres-Méndez, John T Heap
Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria which, as photoautotrophs, are grown under light...
March 15, 2018: ACS Synthetic Biology
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