27 papers · ranked by Valyu relevance
Authors not listed
Accurate and efficient computation of Floquet multipliers and subspaces is essential for analyzing limit cycle in dynamical systems and periodic steady state in Radio Frequency simulation. This problem is typically addressed by solving a periodic linear eigenvalue problem, which is discretized from the linear…
Chinmay A Shukla, Amol A Kulkarni, Ian R Baxendale
The implementation of automation in the multistep flow synthesis is essential for transforming laboratory-scale chemistry into a reliable industrial process. In this review, we briefly introduce the role of automation based on its application in synthesis viz. auto sampling and inline monitoring, optimization and…
S. Ross Glandon, Mahesh Narayanamurthi, Adrian Sandu
Time integration methods for solving initial value problems are an important component of many scientific and engineering simulations. Implicit time integrators are desirable for their stability properties, significantly relaxing restrictions on timestep size. However, implicit methods require solutions to one or more…
Christopher Bresten, Sigal Gottlieb, Zachary Grant, Daniel Higgs + 2 more
'David I. Ketcheson' 'Adrián Németh'] High-order spatial discretizations with strong stability properties (such as monotonicity) are desirable for the solution of hyperbolic PDEs. Methods may be compared in terms of the strong stability preserving (SSP) time-step. We prove an upper bound on the SSP coefficient of…
Samuel N Jator, Leong Lee
A Seventh-Order Linear Multistep Method (SOLMM) is developed and implemented in both predictor-corrector mode and block mode. The two approaches are compared by measuring their total number of function evaluations and CPU times. The stability property of the method is examined. This SOLMM is also compared with existing…
Alan D. Freed
Two-step predictor/corrector methods are provided to solve three classes of problems that present themselves as systems of ordinary differential equations (ODEs). In the first class, velocities are given from which displacements are to be solved. In the second class, velocities and accelerations are given from which…
David D. Hofmann, Gabriele Cozzi, John Fieberg
Integrated step-selection analyses (iSSAs) are versatile and powerful frameworks for studying habitat and movement preferences of tracked animals. iSSAs utilize integrated step-selection functions (iSSFs) to model movements in discrete time, and thus, require animal location data that are regularly spaced in time.…
Yanxue Zhang, Dongmei Zhao, Jinxing Liu
The biggest difficulty of hidden Markov model applied to multistep attack is the determination of observations. Now the research of the determination of observations is still lacking, and it shows a certain degree of subjectivity. In this regard, we integrate the attack intentions and hidden Markov model (HMM) and…
Michael Günther, Adrian Sandu
This survey provides an overview of state-of-the art multirate schemes, which exploit the different time scales in the dynamics of a differential equation model by adapting the computational costs to different activity levels of the system. We start the discussion with the straightforward approach based on…
Khai Chien Lee, Muhammad Naeim Mohd Aris, Ishak Hashim, Norazak Senu
An efficient trigonometrical-fitted two-derivative multistep collocation (TF-TDMC) method using Legendre polynomials up to order five as the basis functions, has been developed for solving second-order ordinary differential equations with oscillatory solution effectively. Interpolation method of approximated power…
Wei Ming, Yukun Bao, Zhongyi Hu, Tao Xiong
The hybrid ARIMA-SVMs prediction models have been established recently, which take advantage of the unique strength of ARIMA and SVMs models in linear and nonlinear modeling, respectively. Built upon this hybrid ARIMA-SVMs models alike, this study goes further to extend them into the case of multistep-ahead prediction…
Mrityunjay K Sharma, Roopashri B Acharya, Chinmay A Shukla, Amol A Kulkarni + 1 more
'Amol A Kulkarni' 'Volker Hessel'] The multistep flow synthesis of complex molecules has gained momentum over the last few years. A wide range of reaction types and conditions have been integrated seamlessly on a single platform including in-line separation as well as monitoring. Beyond merely getting considered as…
Shijie Deng, Brandon Jolly, James Wilkes, Yu Mu + 5 more
Integrated catalysis is an emerging methodology that can streamline the multistep synthesis of complicated products in a single reaction vessel, achieving a high degree of control and reducing the waste and cost of the overall process. Integrated catalysis utilizes spatial and temporal control to couple different…
Qianqian Wu, Tianhai Tian
To deal with the growing scale of molecular systems, sophisticated modelling techniques have been designed in recent years to reduce the complexity of mathematical models. Among them, a widely used approach is delayed reaction for simplifying multistep reactions. However, recent research results suggest that a delayed…
Michael Guenther, Adrian Sandu
This work constructs a new class of multirate schemes based on the recently developed generalized additive Runge-Kutta (GARK) methods [10]. Multirate schemes use different step sizes for different components and for different partitions of the right-hand side based on the local activity levels. We show that the new…
Felix Schwietert, Lina Heydenreich, Jan Kierfeld
Regarding the experimental observation that microtubule catastrophe can be described as a multistep process, we extend the Dogterom–Leibler model for dynamic instability in order to discuss the effect that such a multistep catastrophe mechanism has on the distribution of microtubule lengths in the two regimes of…
Nicholas A. Popp, Rachel L. Powell, Melinda K. Wheelock, Brendan D. Zapp + 11 more
Despite widespread advances in DNA sequencing, the functional consequences of most genetic variants remain poorly understood. Multiplexed Assays of Variant Effect (MAVEs) can measure the function of variants at scale, and are beginning to address this problem. However, MAVEs cannot readily be applied to the ∼10% of…
Jean Sexton, Daniel R. Reynolds
This work focuses on the construction of a new class of fourth-order accurate methods for multirate time evolution of systems of ordinary differential equations. We base our work on the Recursive Flux Splitting Multirate (RFSMR) [1, 2, 3] version of the Multirate Infinitesimal Step (MIS) methods [4, 5, 6, 7, 8], and…
Sebastian Höhna, Allison Y. Hsiang
The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost that would be incurred. Instead, phylogenetic pipelines generally consist of chained analyses…
Sadie Piatt, Allen C. Price
The Generalized Method of Moments (GMM) is a statistical method for the analysis of samples from random processes. First developed for the analysis of econometric data, the method is here formulated to extract hidden kinetic parameters from measurements of single molecule dwell times. Our method is based on the…
Jennifer Pohle, Johannes Signer, Jana A. Eccard, Melanie Dammhahn + 1 more
'Ulrike E. Schlägel'] - 1. Step-selection models are widely used to study animals' fine-scale habitat selection based on movement data. Resource preferences and movement patterns, however, can depend on the animal's unobserved behavioural states, such as resting or foraging. This is ignored in standard (integrated)…
Christopher Lester
Well-designed mechanistic models can provide insights into biological networks that are im-perceptible to machine learning techniques. For example, where suitable experimental data exists, mechanistic models can often provide strong evidence for the causative relationships that underpin a given biological model .…
Authors not listed
Efficient and reliable identification of transition states (TS) is critical for reaction modelling. Among the approaches available, the combination of double-ended TS search with eigenvector-following, referred to as “hierarchical TS search”, is an effective tool to locate TSs starting from reactant and product…
Authors not listed
The rapid growth of worldwide computing power has transformed in silico chemistry into a discipline that is integrated into the daily work of many chemists. Nowadays, researchers find it increasingly straightforward to predict a wide range of molecular properties and chemi- cal processes at reasonable computational…
Yi Sun
We demonstrate how the combination of a shifted clustering algorithm and a fast-marching- based algorithm is able to generate good approximations of the Minimum Free Energy Path (MFEP) if a Free Energy Landscape (FEL) is given. Then, we show that using this kind of approximation as the MFEP's first guess and the string…
Surl-Hee Ahn, Anupam Ojha, Rommie Amaro, James McCammon
Gaussian accelerated molecular dynamics (GaMD) is a well-established enhanced sampling method for molecular dynamics (MD) simulations that effectively samples the potential energy landscape of the system by adding a boost potential, which smoothens the surface and lowers energy barriers between states. Although…
Dayou Zhang, Yinan Shu, Donald G. Truhlar
In this study, we explored several alternative functional forms to construct more accurate and more physical density coherence functionals for multiconfiguration density-coherence functional theory. Each functional is parameterized against the same database as used in our previous work. The best density coherence…