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Theory of simulation

B Tosello, J Blanc, C Kelway, V Pellegrin, E Quarello, F Comte, C Zakarian, C D'Ercole
Though technology plays an increasingly important role in modern health systems, human performance remains a major determinant of safety, effectiveness and efficiency of patient care. This is especially true in the delivery room. Thus, the training of professionals must aim not only for the acquisition of theory and practical skills on an individual basis, but also for the learning of teamwork systematically. Training health professionals with simulation enhances their theoretical knowledge and meets formal requirements in literacy, technical skills and communication...
May 15, 2018: Gynecologie, Obstetrique, Fertilite & Senologie
Reimar H Leike, Torsten A Enßlin
Most simulation schemes for partial differential equations (PDEs) focus on minimizing a simple error norm of a discretized version of a field. This paper takes a fundamentally different approach; the discretized field is interpreted as data providing information about a real physical field that is unknown. This information is sought to be conserved by the scheme as the field evolves in time. Such an information theoretic approach to simulation was pursued before by information field dynamics (IFD). In this paper we work out the theory of IFD for nonlinear PDEs in a noiseless Gaussian approximation...
March 2018: Physical Review. E
Subhajit Paul, Subir K Das
Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling granular gas model (GGM), for each of which we quantify the time dependence of kinetic energy and average mass of clusters (that form due to inelastic collisions). These quantities, for both the models, exhibit power-law behavior, at least in the long time limit. For the BAM, corresponding exponents exhibit strong dimension dependence and follow a hyperscaling relation...
March 2018: Physical Review. E
Reza Haghani Hassan Abadi, Abbas Fakhari, Mohammad Hassan Rahimian
In this paper, we propose a multiphase lattice Boltzmann model for numerical simulation of ternary flows at high density and viscosity ratios free from spurious velocities. The proposed scheme, which is based on the phase-field modeling, employs the Cahn-Hilliard theory to track the interfaces among three different fluid components. Several benchmarks, such as the spreading of a liquid lens, binary droplets, and head-on collision of two droplets in binary- and ternary-fluid systems, are conducted to assess the reliability and accuracy of the model...
March 2018: Physical Review. E
Shanshan Qin, Chao Tang
Complex dynamical systems often have tipping points and exhibit catastrophic regime shift. Despite the notorious difficulty of predicting such transitions, accumulating studies have suggested the existence of generic early-warning signals (EWSs) preceding upcoming transitions. However, previous theories and models were based on the effect of the intrinsic noise (IN) when a system is approaching a critical point, and did not consider the pervasive environmental fluctuations or the extrinsic noise (EN). Here, we extend previous theory to investigate how the interplay of EN and IN affects EWSs...
March 2018: Physical Review. E
Michele Monti, David K Lubensky, Pieter Rein Ten Wolde
Circadian clocks are biochemical oscillators that allow organisms to estimate the time of the day. These oscillators are inherently noisy due to the discrete nature of the reactants and the stochastic character of their interactions. To keep these oscillators in sync with the daily day-night rhythm in the presence of noise, circadian clocks must be coupled to the dark-light cycle. In this paper, we study the entrainment of phase oscillators as a function of the intrinsic noise in the system. Using stochastic simulations, we compute the optimal coupling strength, intrinsic frequency, and shape of the phase-response curve, that maximize the mutual information between the phase of the clock and time...
March 2018: Physical Review. E
Fabio C Zegarra, Dirar Homouz, Yossi Eliaz, Andrei G Gasic, Margaret S Cheung
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α/β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β-barrel α-spectrin Src-homology 3 domain (SH3) protein...
March 2018: Physical Review. E
Taketo Ariki, Kyo Yoshida, Keigo Matsuda, Katsunori Yoshimatsu
Heavy particle clustering in turbulence is discussed from both phenomenological and analytical points of view, where the -4/3 power law of the pair-correlation function is obtained in the inertial range. A closure theory explains the power law in terms of the balance between turbulence mixing and preferential-concentration mechanism. The obtained -4/3 power law is supported by a direct numerical simulation of particle-laden turbulence.
March 2018: Physical Review. E
Zhi-Rui Zhou, You-Sheng Zhang, Bao-Lin Tian
Implicit large eddy simulations of two-dimensional Rayleigh-Taylor instability at different density ratios (i.e., Atwood number A=0.05, 0.5, and 0.9) are conducted to investigate the late-time dynamics of bubbles. To produce a flow field full of bounded, semibounded, and chaotic bubbles, three problems with distinct perturbations are simulated: (I) periodic sinusoidal perturbation, (II) isolated W-shaped perturbation, and (III) random short-wave perturbations. The evolution of height h, velocity v, and diameter D of the (dominant) bubble with time t are formulated and analyzed...
March 2018: Physical Review. E
S V Batalov, A G Shagalov, L Friedland
Controlling the state of a Bose-Einstein condensate driven by a chirped frequency perturbation in a one-dimensional anharmonic trapping potential is discussed. By identifying four characteristic time scales in this chirped-driven problem, three dimensionless parameters P_{1,2,3} are defined describing the driving strength, the anharmonicity of the trapping potential, and the strength of the particles interaction, respectively. As the driving frequency passes the linear resonance in the problem, and depending on the location in the P_{1,2,3} parameter space, the system may exhibit two very different evolutions, i...
March 2018: Physical Review. E
Parth Rakesh Desai, Shayandev Sinha, Siddhartha Das
We employ molecular dynamics (MD) simulations and develop scaling theories to quantify the equilibrium behavior of polyelectrolyte (PE) brush bilayers (BBLs) in the weakly interpenetrated regime, which is characterized by d_{0}<d_{g}<2d_{0}, where d_{g} is the gap between the opposing plates where the PE brushes are grafted and d_{0} is the unperturbed height of a PE brush grafted at a single plate. Scaling predictions establish that, for the weakly interpenetrated osmotic PE BBLs δ∼N^{1/2}(2-d_{g}/d_{0})^{1/2} (where δ is the interpenetration length and N is the number of Kuhn segments in PE brush)...
March 2018: Physical Review. E
Hyosub Kim, YeJe Park, Kyungtae Kim, H-S Sim, Jaewook Ahn
Dynamics of large complex systems, such as relaxation towards equilibrium in classical statistical mechanics, often obeys a master equation that captures essential information from the complexities. Here, we find that thermalization of an isolated many-body quantum state can be described by a master equation. We observe sudden quench dynamics of quantum Ising-like models implemented in our quantum simulator, defect-free single-atom tweezers in conjunction with Rydberg-atom interaction. Saturation of their local observables, a thermalization signature, obeys a master equation experimentally constructed by monitoring the occupation probabilities of prequench states and imposing the principle of the detailed balance...
May 4, 2018: Physical Review Letters
Hao Wang, Weitao Yang
We developed a novel neural network based force field for water based on training with high level ab initio theory. The force field was built based on electrostatically embedded many-body expansion method truncated at binary interactions. Many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach...
May 18, 2018: Journal of Physical Chemistry Letters
Projesh Kumar Roy, Markus Heyde, Andreas Heuer
The recent experimental discovery of a semi two-dimensional silica glass has offered a realistic description of the random network theory of a silica glass structure, initially discussed by Zachariasen. To study the structure formation of silica in two dimensions, we introduce a two-body force field, based on a soft core Yukawa potential. The different configurations, sampled via Molecular dynamics simulations, can be directly compared with the experimental structures, which have been provided in the literature...
May 18, 2018: Physical Chemistry Chemical Physics: PCCP
Mitchell Goldenberg, Jason Y Lee
PURPOSE OF REVIEW: Competency-based medical education (CBME) is rooted in the use of iterative assessments. We must ensure that the assessments used in CBME are valid, to make acceptable and accurate decisions regarding the competency of a trainee. Until recently, much of the educational and assessment literature in urology have used a now-outdated method of determining validity, based on theory and recommendations from over 50 years ago. We describe a contemporary approach to gathering construct validity evidence for the assessment of urologic trainees, for use in both clinical and simulation environments...
May 17, 2018: Current Urology Reports
Daniele Coslovich, Misaki Ozawa, Walter Kob
The physical behavior of glass-forming liquids presents complex features of both dynamic and thermodynamic nature. Some studies indicate the presence of thermodynamic anomalies and of crossovers in the dynamic properties, but their origin and degree of universality is difficult to assess. Moreover, conventional simulations are barely able to cover the range of temperatures at which these crossovers usually occur. To address these issues, we simulate the Kob-Andersen Lennard-Jones mixture using efficient protocols based on multi-CPU and multi-GPU parallel tempering...
May 17, 2018: European Physical Journal. E, Soft Matter
Daryna Smyrnova, María Del Carmen Marín, Massimo Olivucci, Arnout Ceulemans
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40~nm in absorption maxima and only 18~nm in emission. The five proteins -- Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa -- carry exactly the same chromophore and differ just in a few mutations. Thus they form an ideal set for mechanistic investigation. Starting with the results of molecular dynamics simulations we use QM/MM calculations to investigate the effects controlling the spectral tuning . In this contribution we show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed absorption trend with only a limited blue-shift of 4...
May 17, 2018: Journal of Chemical Theory and Computation
Zhanshan Wang, Lei Liu, Yanming Wu, Huaguang Zhang
This paper investigates the problem of optimal fault-tolerant control (FTC) for a class of unknown nonlinear discrete-time systems with actuator fault in the framework of adaptive critic design (ACD). A pivotal highlight is the adaptive auxiliary signal of the actuator fault, which is designed to offset the effect of the fault. The considered systems are in strict-feedback forms and involve unknown nonlinear functions, which will result in the causal problem. To solve this problem, the original nonlinear systems are transformed into a novel system by employing the diffeomorphism theory...
June 2018: IEEE Transactions on Neural Networks and Learning Systems
Huaguang Zhang, Qiuxia Qu, Geyang Xiao, Yang Cui
Based on integral sliding mode and approximate dynamic programming (ADP) theory, a novel optimal guaranteed cost sliding mode control is designed for constrained-input nonlinear systems with matched and unmatched disturbances. When the system moves on the sliding surface, the optimal guaranteed cost control problem of sliding mode dynamics is transformed into the optimal control problem of a reformulated auxiliary system with a modified cost function. The ADP algorithm based on single critic neural network (NN) is applied to obtain the approximate optimal control law for the auxiliary system...
June 2018: IEEE Transactions on Neural Networks and Learning Systems
Keith Wachowicz, Brad Murray, B Gino Fallone
The recent interest in the integration of external beam radiotherapy with a magnetic resonance (MR) imaging unit offers the potential for real-time adaptive tumour tracking during radiation treatment. The tracking of large tumours which follow a rapid trajectory may best be served by the generation of a projection image from the perspective of the beam source, or "beam's eye view" (BEV). This type of image projection represents the path of the radiation beam, thus enabling rapid compensations for target translations, rotations and deformations, as well time-dependent critical structure avoidance...
May 17, 2018: Physics in Medicine and Biology
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