相关论文: A Formulation of the Ring Polymer Molecular Dynami…
The reaction between D$^+$ and H$_2$ plays an important role in astrochemistry at low temperatures and also serves as a prototype for simple ion-molecule reaction. Its ground $\tilde{X}~^1A^{\prime}$ state has a very small thermodynamic…
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…
We report a novel multi-scale simulation methodology to quantitatively predict the thermodynamic behaviour of polymer mixtures, that exhibit phases with broken orientational symmetry. Our system consists of a binary mixture of oligomers and…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Polymer dynamics is analyzed through the lens of linear dimensionality reduction methods, in particular principal (PCA) and time-lagged independent component analysis (tICA). For a polymer undergoing ideal Rouse dynamics, the slow modes…
In collider experiments, an event is characterized by two distinct yet mutually complementary features: the `global features' and the `local features'. Kinematic information such as the event topology of a hard process, masses, and spins of…
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrating Kramers' theory with Bell's equation,…
The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations,…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
Classical and path integral molecular dynamics (PIMD) simulations are used to study alpha-quartz and beta-quartz in a large range of temperatures at zero external stress. PIMD account for quantum fluctuations of atomic vibrations, which can…
We revisit the evolution of generalised parton distributions (GPDs) in momentum space. We formulate the evolution kernels at one-loop in perturbative QCD (pQCD) in a form suitable for numerical implementation and that allows for an accurate…
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…
The configuration of most robotic systems lies in continuous transformation groups. However, in mobile robot trajectory tracking, many recent works still naively utilize optimization methods for elements in vector space without considering…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
The Hamiltonian for a small number, N <= 11, of bosons in a rapidly rotating harmonic trap, interacting via a short range (contact potential) or a long range (Coulomb) interaction, is studied via an exact diagonalization in the lowest…
We develop an algorithm for bosonic path integral molecular dynamics (PIMD) simulations with periodic boundary conditions (PBC) that scales quadratically with the number of particles. Path integral methods are a powerful tool to simulate…
Molecular dynamics with electronic friction (MDEF) approach can describe nonadiabatic effects accurately at metal surfaces in the weak nonadiabatic limit. That being said, MDEF treats nuclear motion classically, such that the nuclear…
Quantum dynamics simulations of reactive molecular processes are commonly performed in a low-dimensional space spanned by highly optimized reactive coordinates. Usually, these sets of reactive coordinates consist of non-linear coordinates.…
In this paper, we propose a whole-body planning framework that unifies dynamic locomotion and manipulation tasks by formulating a single multi-contact optimal control problem. We model the hybrid nature of a generic multi-limbed mobile…
Quantum Molecular Dynamics (QMD) calculations of central collisions between heavy nuclei are used to study fragment production and the creation of collective flow. It is shown that the final phase space distributions are compatible with the…