Integration Step Research Articles

Assessing parameters for ring polymer molecular dynamics simulations at low temperatures: DH + H chemical reaction

Ring polymer molecular dynamics (RPMD) is an accurate method for calculating thermal chemical reaction rates. It has recently been discovered that low-temperature calculations are strongly affected by the simulation parameters. Here, for the thermally activated reaction DH + H → D + H2, we calculate the RPMD rate constants at T=50, 100, and 300 K and demonstrate that for T≥100 K the standard input parameters yield accurate results, but at low temperatures (e.g., 50 K) one must increase the asymptotic distance and force constant, and decrease the umbrella integration step.

Integrasi Iptek Dengan Imtaq pada Pelajaran MIA di MAN Insan Cendekia Tapanuli Selatan

The dichotomy of science in madrasa, science and technology material has not been integrated with Islam and vice versa. Habibie founded Insan Scholar to unite IPTEK with IMTAQ, and MAN IC South Tapanuli was no exception. This study aims to describe, discover, and explain the integration of IPTEK white IMTAQ of MIA subject groups in MAN Insan Cendekia South Tapanuli. The conclusions of this study are: The curriculum integration implemented at MAN Insan Cendekia South Tapanuli is the development of a curriculum set by the government. There are two patterns used by teachers in curriculum integration, namely Islamization of general science, and Spiritualization of learning. This can be seen from the integration steps contained in the plan, implementation, and evaluation of the program, namely: 1) Read greetings and prayers, 2) Apperception and ensure students memorize Qur’an and Hadith, 3) Review material from a general and Islamic angle, 4) Bringing students out of the room for natural learning, 5) Providing exercises and questions that can improve IPTEK and IMTAQ, 6) Motivation and re-awareness that all truth comes from God, 7) Closed with Kafaratul Majelis prayers and greetings.

Stability of real-time hybrid simulation involving time-varying delay and direct integration algorithms

Stability presents a critical issue for real-time hybrid simulation. Actuator delay might destabilize the real-time test without proper compensation. Previous research often assumed real-time hybrid simulation as a continuous-time system; however, it is more appropriately treated as a discrete-time system because of application of digital devices and integration algorithms. By using the Lyapunov–Krasovskii theory, this study explores the convoluted effect of integration algorithms and actuator delay on the stability of real-time hybrid simulation. Both theoretical and numerical analysis results demonstrate that (1) the direct integration algorithm is preferably used for real-time hybrid simulation because of its computational efficiency; (2) the stability analysis of real-time hybrid simulation highly depends on actuator delay models, and the actuator model that accounts for time-varying characteristic will lead to more conservative stability; and (3) the integration step is constrained by the algorithm and structural frequencies. Moreover, when the step is small, the stability of the discrete-time system will approach that of the corresponding continuous-time system. The study establishes a bridge between continuous- and discrete-time systems for stability analysis of real-time hybrid simulation.

Toward Understanding the Growth of Cefradine in Aqueous Solution

Crystal growth, which is one of the fundamental steps in the crystallization process, can affect the morphology of crystals which will further affect physicochemical properties of products and downstream processing. In this study, crystal growth of cefradine in aqueous solution was systematically investigated by combining experimental methods and molecular dynamics simulations. Single crystal growth experiments were adopted to obtain the growth kinetics data of cefradine in water. Growth kinetics models considering the bulk diffusion step and surface integration step were applied to evaluate the experimental data. Surface chemistry, Connolly surface, radial distribution function, and electrostatic potential were calculated through molecular dynamics simulation to further explore the growth kinetics from the molecular level. The results revealed that water molecules preferred to be adsorbed onto the (1 0 1) crystal face than the (0 1 1) and (0 1̅ 1) surfaces due to the favored hydrophilicity and solvent adsorption sites. In addition, the stronger interaction between water molecules and the (1 0 1) crystal face by electrostatic and hydrogen-bonding interactions would further highly hinder the crystal growth along the radial direction. Finally, a possible growth mechanism based on blocking effect of solvent molecules was proposed to interpret the different growth kinetics along the axial and radial directions.

МОДЕЛЮВАННЯ ПОВЕДІНКИ СТРИЖНЯ З ТРИЛІНІЙНОГО ДВОФАЗНОГО МАТЕРІАЛУ З УРАХУВАННЯМ ТЕМПЕРАТУРИ

В роботі сформульовано феноменологічну модель для опису властивостей сплавів із пам’яттю форм та пам’яттю в точці зміни температури. Встановлено, що класичні матеріальні діаграми – це конверт певного сімейства матеріальних діаграм, побудований за певнимизаконами зміни швидкості та розриву фронту деформації. Для використання феноменологічної моделі з метою дослідження двофазних матеріалів з різними модулями пружності розв’язано додаткову задачу, яка пов’язана з розбудовою миттєвої термомеханічної поверхні. В роботі проведено числове дослідження, як результат показано типову залежність для швидкості розповсюдження фазового переходу від часу. Графік залежності має три ділянки. На першій ділянці швидкість дорівнює нулю, а на третій – досягає постійного значення. Між ними міститься ділянка зі змінною швидкістю. В результаті обчислення дотичного модуля на кожному кроці інтегрування за часом інтегральна діаграма матеріалу, побудована в роботі, теж має три характерні ділянки.

HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants.

Integrase strand transfer inhibitors (INSTIs) block the integration step of the retroviral lifecycle and are first-line drugs used for the treatment of HIV-1/AIDS. INSTIs have a polycyclic core with heteroatom triads, chelate the metal ions at the active site, and have a halobenzyl group that interacts with viral DNA attached to the core by a flexible linker. The most broadly effective INSTIs inhibit both wild-type (WT) integrase (IN) and a variety of well-known mutants. However, because there are mutations that reduce the potency of all of the available INSTIs, new and better compounds are needed. Models based on recent structures of HIV-1 and red-capped mangabey SIV INs suggest modifications in the INSTI structures that could enhance interactions with the 3′-terminal adenosine of the viral DNA, which could improve performance against INSTI resistant mutants. We designed and tested a series of INSTIs having modifications to their naphthyridine scaffold. One of the new compounds retained good potency against an expanded panel of HIV-1 IN mutants that we tested. Our results suggest the possibility of designing inhibitors that combine the best features of the existing compounds, which could provide additional efficacy against known HIV-1 IN mutants.

A finite volume method for two-moment cosmic ray hydrodynamics on a moving mesh

ABSTRACT We present a new numerical algorithm to solve the recently derived equations of two-moment cosmic ray hydrodynamics (CRHD). The algorithm is implemented as a module in the moving mesh Arepo code. Therein, the anisotropic transport of cosmic rays (CRs) along magnetic field lines is discretized using a path-conservative finite volume method on the unstructured time-dependent Voronoi mesh of Arepo. The interaction of CRs and gyroresonant Alfvén waves is described by short time-scale source terms in the CRHD equations. We employ a custom-made semi-implicit adaptive time stepping source term integrator to accurately integrate this interaction on the small light-crossing time of the anisotropic transport step. Both the transport and the source term integration step are separated from the evolution of the magnetohydrodynamical equations using an operator split approach. The new algorithm is tested with a variety of test problems, including shock tubes, a perpendicular magnetized discontinuity, the hydrodynamic response to a CR overpressure, CR acceleration of a warm cloud, and a CR blast wave, which demonstrate that the coupling between CR and magnetohydrodynamics is robust and accurate. We demonstrate the numerical convergence of the presented scheme using new linear and non-linear analytic solutions.

Nonlinear dynamics of rectangular nano-shells

Mathematical model of non-linear vibrations of shallow, elastic, isotropic nano-shells with rectangular base subjected to transverse sign-variable load are constructed. Based on Kirchhoff-Love thin shell theory with von Kármán nonlinear strains and the modified couple stress theory (MCST), size-dependent governing equations and corresponding boundary conditions are established through Hamilton’s principle. The governing PDEs are reduced to ODEs by the second-order Finite Difference Method (FDM). The obtained system of equations is solved by Runge–Kutta methods of second order accuracy. The Cauchy problem is solved by the Runge–Kutta fourth-order method. We analyzed the convergence of these solutions depending on the step of integration over time and spatial coordinate. It was revealed, that taking into account nano-effects increases area of harmonic vibrations and leads to the appearance of as chaotic and hyperchaotic vibrations. The carried out numerical experiment shows, that the transition of vibrations from harmonic to chaotic follows to Feigenbaum’s scenario. In particular, to analyze the character type of vibration computation of largest Lyapunov exponents are employed. We found that hyperchaotic vibrations are characterized by two positive Lyapunov exponents and chaotic vibration by one positive Lyapunov exponent. For nano-shells, this phenomenon was discovered for the first time. Lyapunov exponents spectra estimated by different algorithms, including Wolf’s, Rosenstein’s, Kantz’s, and Sawada. Numerical examples of the theoretical investigations are given.

Analysis of unilateral event-continuous systems

Numerical analysis of unilateral event-continuous processes in comparison with traditional simulation algorithms for discrete-continuous systems is addressed. An original integration step size control algorithm guaranteeing correct detection of unilateral events is given. The algorithm is tested on a typical problem. Simulations are carried out in modern computer environments for modeling and simulation of complex dynamic systems of the mentioned class. A comparative analysis of the application of the software environments to event-continuous processes with unilateral events is presented.

The On-Line Integrated Mesoscale Chemistry Model BOLCHEM

This work presents the on-line coupled meteorology–chemistry transport model BOLCHEM, based on the hydrostatic meteorological BOLAM model, the gas chemistry module SAPRC90, and the aerosol dynamic module AERO3. It includes parameterizations to describe natural source emissions, dry and wet removal processes, as well as the transport and dispersion of air pollutants. The equations for different processes are solved on the same grid during the same integration step, by means of a time-split scheme. This paper describes the model and its performance at horizontal resolution of 0.2∘× 0.2∘ over Europe and 0.1∘× 0.1∘ in a nested configuration over Italy, for one year run (December 2009–November 2010). The model has been evaluated against the AIRBASE data of the European Environmental Agency. The basic statistics for higher resolution simulations of O3, NO2 and particulate matter concentrations (PM2.5 and PM10) have been compared with those from Copernicus Atmosphere Monitoring Service (CAMS) ensemble median. In summer, for O3 we found a correlation coefficient R of 0.72 and mean bias of 2.15 over European domain and a correlation coefficient R of 0.67 and mean bias of 2.36 over Italian domain. PM10 and PM2.5 are better reproduced in the winter, the latter with a correlation coefficient R of 0.66 and the mean bias MB of 0.35 over Italian domain.

Imaging Viral Infection by Fluorescence Microscopy: Focus on HIV-1 Early Stage.

During the last two decades, progresses in bioimaging and the development of various strategies to fluorescently label the viral components opened a wide range of possibilities to visualize the early phase of Human Immunodeficiency Virus 1 (HIV-1) life cycle directly in infected cells. After fusion of the viral envelope with the cell membrane, the viral core is released into the cytoplasm and the viral RNA (vRNA) is retro-transcribed into DNA by the reverse transcriptase. During this process, the RNA-based viral complex transforms into a pre-integration complex (PIC), composed of the viral genomic DNA (vDNA) coated with viral and host cellular proteins. The protective capsid shell disassembles during a process called uncoating. The viral genome is transported into the cell nucleus and integrates into the host cell chromatin. Unlike biochemical approaches that provide global data about the whole population of viral particles, imaging techniques enable following individual viruses on a single particle level. In this context, quantitative microscopy has brought original data shedding light on the dynamics of the viral entry into the host cell, the cytoplasmic transport, the nuclear import, and the selection of the integration site. In parallel, multi-color imaging studies have elucidated the mechanism of action of host cell factors implicated in HIV-1 viral cycle progression. In this review, we describe the labeling strategies used for HIV-1 fluorescence imaging and report on the main advancements that imaging studies have brought in the understanding of the infection mechanisms from the viral entry into the host cell until the provirus integration step.

Higher order Hamiltonian Monte Carlo sampling for cosmological large-scale structure analysis

ABSTRACT We investigate higher order symplectic integration strategies within Bayesian cosmic density field reconstruction methods. In particular, we study the fourth-order discretization of Hamiltonian equations of motion (EoM). This is achieved by recursively applying the basic second-order leap-frog scheme (considering the single evaluation of the EoM) in a combination of even numbers of forward time integration steps with a single intermediate backward step. This largely reduces the number of evaluations and random gradient computations, as required in the usual second-order case for high-dimensional cases. We restrict this study to the lognormal-Poisson model, applied to a full volume halo catalogue in real space on a cubical mesh of 1250 h−1 Mpc side and 2563 cells. Hence, we neglect selection effects, redshift space distortions, and displacements. We note that those observational and cosmic evolution effects can be accounted for in subsequent Gibbs-sampling steps within the COSMIC BIRTH algorithm. We find that going from the usual second to fourth order in the leap-frog scheme shortens the burn-in phase by a factor of at least ∼30. This implies that 75–90 independent samples are obtained while the fastest second-order method converges. After convergence, the correlation lengths indicate an improvement factor of about 3.0 fewer gradient computations for meshes of 2563 cells. In the considered cosmological scenario, the traditional leap-frog scheme turns out to outperform higher order integration schemes only when considering lower dimensional problems, e.g. meshes with 643 cells. This gain in computational efficiency can help to go towards a full Bayesian analysis of the cosmological large-scale structure for upcoming galaxy surveys.

Babel: A Generic Benchmarking Platform for Big Data Architectures

In this era of big and fast data, software architects tend to find it really hard to make consistent decisions about which architecture and technologies are ideal for a certain business need. It is even harder to make them while dealing with the scarcity of clear methodologies, best practices and reference architectures. In this prospect, architecture evaluation through benchmarking can be of great interest, as it enables the detection of performance anomalies or bottlenecks as you go. The problem when talking about Big Data benchmarking, is that existing solutions remain technology-related, and do not deal with the heterogeneous aspect of complex architectures. In addition to that, businesses are in general dealing with multi-layered complex systems, involving various technologies, paradigms and micro-architectures. This means that the benchmarking solution must be able to give fine-grained insights about each of the layers. A successful benchmarking system must also be seamless, easy to use, scalable, and preferably cloud native. To satisfy these requirements, we designed and implemented Babel, a generic Big Data benchmarking platform, that insures an end-to-end performance evaluation and monitoring. We present in this paper the principles, architecture, integration and deployment steps of Babel.

Numerical Method for Coupled Nonlinear Schrödinger Equations in Few-Mode Fiber

This paper discusses novel approaches to the numerical integration of the coupled nonlinear Schrödinger equations system for few-mode wave propagation. The wave propagation assumes the propagation of up to nine modes of light in an optical fiber. In this case, the light propagation is described by the non-linear coupled Schrödinger equation system, where propagation of each mode is described by own Schrödinger equation with other modes’ interactions. In this case, the coupled nonlinear Schrödinger equation system (CNSES) solving becomes increasingly complex, because each mode affects the propagation of other modes. The suggested solution is based on the direct numerical integration approach, which is based on a finite-difference integration scheme. The well-known explicit finite-difference integration scheme approach fails due to the non-stability of the computing scheme. Owing to this, here we use the combined explicit/implicit finite-difference integration scheme, which is based on the implicit Crank–Nicolson finite-difference scheme. It ensures the stability of the computing scheme. Moreover, this approach allows separating the whole equation system on the independent equation system for each wave mode at each integration step. Additionally, the algorithm of numerical solution refining at each step and the integration method with automatic integration step selection are used. The suggested approach has a higher performance (resolution)—up to three times or more in comparison with the split-step Fourier method—since there is no need to produce direct and inverse Fourier transforms at each integration step. The key advantage of the developed approach is the calculation of any number of modes propagated in the fiber.

A collocation methods based on the quadratic quadrature technique for fractional differential equations

<abstract><p>In this paper, we introduce a mixed numerical technique for solving fractional differential equations (FDEs) by combining Chebyshev collocation methods and a piecewise quadratic quadrature rule. For getting solutions at each integration step, the fractional integration is calculated in two intervals-all previous time intervals and the current time integration step. The solution at the current integration step is calculated by using Chebyshev interpolating polynomials. To remove a singularity which belongs originally to the FDEs, Lagrangian interpolating technique is considered since the Chebyshev interpolating polynomial can be rewritten as a Lagrangian interpolating form. Moreover, for calculating the fractional integral on the whole previous time intervals, a piecewise quadratic quadrature technique is applied to get higher accuracy. Several numerical experiments demonstrate the efficiency of the proposed method and show numerically convergence orders for both linear and nonlinear cases.</p></abstract>

Fast Simulation and Chaos Investigation of a DC‐DC Boost Inverter

Intensive and repetitive simulations are required to study static and dynamic behaviours of systems. Particular phenomena such as bifurcation and chaos require long simulation times and analysis. To check the existence of bifurcations and chaos in a dynamic system, a fine‐tuning procedure of a bifurcation parameter is to be carried out. This increases considerably the computing time, and a great amount of patience is needed to obtain adequate results. Because of the high switching frequency of a boost inverter, the integration process of the dynamic model used to describe it uses an integration step that is in general less than one microsecond. This makes the integration process time consuming even for a short simulation. Thus, a fast, but accurate, method is suitable to analyse the dynamic behaviour of the converter. This work contains two topics. First, we develop a like‐discrete integration process that permits precise results in a very fast manner. For one switching period, we compute only two or a maximum of three breaking points depending on whether we treat a continuous conduction mode (CCM) or a discontinuous conduction mode (DCM) of the inductor current. Furthermore, with each segment of the dynamic trajectory, an exact analytic formula is associated. The second goal is to use this result to develop a discrete iterative map formulated as in standard discrete time series models. The Jacobian matrix of the found iterative map is defined and used to compute Lyapunov exponents to prove existence of chaos. Performance of the developed study is positively evaluated by using classical simulations and fine‐tuning a bifurcation parameter to detect chaos. This parameter is the desired reference of the inductor current peak. Results show that the proposed scheme is very fast and accurate. The study can be easily extended to other switching topologies of DC‐DC inverters.

Optimized binding of substituted quinoline ALLINIs within the HIV-1 integrase oligomer

During the integration step, human immunodeficiency virus type 1 integrase (IN) interacts with viral DNA and the cellular cofactor LEDGF/p75 to effectively integrate the reverse transcript into the host chromatin. Allosteric human immunodeficiency virus type 1 integrase inhibitors (ALLINIs) are a new class of antiviral agents that bind at the dimer interface of the IN catalytic core domain and occupy the binding site of LEDGF/p75. While originally designed to block IN-LEDGF/p75 interactions during viral integration, several of these compounds have been shown to also severely impact viral maturation through an IN multimerization mechanism. In this study, we tested the hypothesis that these dual properties of ALLINIs could be decoupled toward late stage viral replication effects by generating additional contact points between the bound ALLINI and a third subunit of IN. By sequential derivatization at position 7 of a quinoline-based ALLINI scaffold, we show that IN multimerization properties are enhanced by optimizing hydrophobic interactions between the compound and the C-terminal domain of the third IN subunit. These features not only improve the overall antiviral potencies of these compounds but also significantly shift the ALLINIs selectivity toward the viral maturation stage. Thus, we demonstrate that to fully maximize the potency of ALLINIs, the interactions between the inhibitor and all three IN subunits need to be simultaneously optimized.

Efficient Approach for Atmospheric Phase Screen Mitigation in Time Series of Terrestrial Radar Interferometry Data Applied to Measure Glacier Velocity

The accuracy of surface displacements measured by differential radar interferometry is significantly degraded by the atmospheric phase screen (APS). This article presents a practical and efficient approach for APS mitigation based on the coherent pixels technique (CPT) displacement velocity estimation algorithm. In the proposed approach, all motionless coherent pixels closest to the moving area are defined as seeds surrounding the moving area at the integration step of the CPT. This arrangement consequently minimizes the integration path and the APS effect in the final velocity result. It is designed for terrestrial radar interferometry (TRI) applications. A piecewise processing chain is further introduced as a continuous operational mode processing framework to derive arbitrary temporal displacement patterns in this work. Three-day datasets measured by Ku-band TRI over a mountainous region in the canton of Valais, Switzerland, were used for validation. Through this validation, a comparative study of five algorithms was carried out. This evaluation showed the efficiency of the proposed approach. The proposed approach does not require phase unwrapping, kriging interpolation, and spatio-temporal covariance inference for APS mitigation, which is appropriate for continuous TRI operation.

Deep Attention on Measurable and Behavioral-driven Complete Service Composition Design Process

The web service technology has still proved its effectiveness in the digital revolution we are facing. This success unfortunately raises more and more complex obstacles, particularly related to the service composition. The integration of Non-Functional Requirements (NFRs) in each step of service composition process, starting with abstract service composition specification to the generation of the verified and concrete composed services, represents one of them. Furthermore, this complexity remains more difficult when NFRs are addressed in both quantifiable (i.e. Quality of Service) and behavioral aspects. Despite the relevant contributions present in the literature, this challenge still remains an open issue when considering NFRs modeling, publishing, integrating with each other, and handling conflicts and dependencies in the whole composition’s lifecycle. As a consequence, we suggest this contribution that aims to propose an approach showing how to weave efficiently required NFRs with functional requirements in a complete lifecycle composition supporting specification, formalization, model checking verification and integration steps of desired concrete composite service. Patient Health Records in Regional and University Health Centers in Morocco is used as a case study to experiment our approach.

Local high-order conservative space-time adaptive mesh refinement with the Runge-Kutta time integration for solving the systems of conservation laws

Numerical simulation is widely used as a main way of researching the processes described by the systems of partial differential equations in the divergence form, like fluid dynamics, traffic flow, wave propagation. To obtain desired accuracy and resolution, the high-order numerical methods are used. In this paper we consider the Runge-Kutta (RK) time discretization, when the space discretization can be high-order finite volume method, discontinuous Galerkin method or others. Presence of discrete analogue of conservation is considered to be very important for such methods as it corresponds to the essential feature of simulated process, becoming especially vital at the discontinuous solutions. The adaptive mesh refinement (AMR) techniques are used to get the numerical solution with more resolution where needed. For the explicit numerical scheme obeying the Courant-Friedrichs-Lewy (CFL) condition, the bigger time integration step can be chosen for the coarser cells. The problem is how to reformulate the numerical scheme near the boundary between cells of different size, keeping the conservation and high-order accuracy. In this paper a new algorithm is suggested. The changes in the numerical method are made only in the vicinity of the boundary. The local character of the developed algorithm allows us to efficiently implement it at modern computer systems. Results of validation tests of developed solver are shown.