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Parallel kinematic manipulators (PKM) are characterized by closed kinematic loops, due to the parallel arrangement of limbs but also due to the existence of kinematic loops within the limbs. Moreover, many PKM are built with limbs…
The accurate and efficient calculation of the rate coefficients of chemical reactions is a key issue in the research of chemical dynamics. In this work, by applying the dimension-free ultra-stable Cayley propagator, the thermal rate…
We develop a novel multilevel asymptotic-preserving Monte Carlo method, called Multilevel Kinetic-Diffusion Monte Carlo (ML-KDMC), for simulating the kinetic Boltzmann transport equation with a Bhatnagar-Gross-Krook (BGK) collision…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…
G-protein-coupled receptors (GPCRs), primary targets for over one-third of approved therapeutics, rely on intricate conformational transitions to transduce signals. While Molecular Dynamics (MD) is essential for elucidating this…
This paper is devoted to the numerical symplectic approximation of the charged-particle dynamics (CPD) with arbitrary electromagnetic fields. By utilizing continuous-stage methods and exponential integrators, a general class of symplectic…
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
Kinodynamic Motion Planning (KMP) is to find a robot motion subject to concurrent kinematics and dynamics constraints. To date, quite a few methods solve KMP problems and those that exist struggle to find near-optimal solutions and exhibit…
A novel quantum dynamical method to simulate vibronic reaction dynamics in molecules at metal surfaces is proposed. The method is based on the hierarchical quantum master equation approach and uses a discrete variable representation of the…
This technical report provides an in-depth evaluation of both established and state-of-the-art methods for simulating constrained rigid multi-body systems with hard-contact dynamics, using formulations of Nonlinear Complementarity Problems…
An accurate description of nonadiabatic dynamics of molecular species on metallic surfaces poses a serious computational challenge associated with a multitude of closely-spaced electronic states. We propose a mixed quantum-classical scheme…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
A high-fidelity kinetic Monte Carlo (KMC) simulation method (T. Treeratanaphitak, M. Pritzker, N. M. Abukhdeir, Electrochim. Acta 121 (2014) 407--414) using the semi-empirical multi-body embedded-atom method (EAM) potential has been…
We present parameter-interpolated dynamic mode decomposition (piDMD), a parametric reduced-order modeling framework that embeds known parameter-affine structure directly into the DMD regression step. Unlike existing parametric DMD methods…
Globally accurate full-dimensional ground state potential energy surface (PES) for the Cl($^2$P) + XCl $\to$ HCl + Cl($^2$P) reaction, a prototypical heavy-light-heavy abstract reaction, is developed using permutation invariant polynomial…
Developing new methods for the accurate and efficient calculations of real-time quantum correlation functions is deemed one of the most challenging problems of modern condensed matter theory. Many popular methods, such as centroid molecular…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…