相关论文: Kinetic distance and kinetic maps from molecular d…
Dimensionality reduction techniques have found great success in a wide range of fields requiring analysis of high-dimensional datasets. Time-lagged independent components analysis (TICA), which finds independent components (TICs) with…
A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involved in these processes, and (ii) estimation of the rates or…
A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly-varying collective variables, where subsequent analyses are made, such as…
Markov state models (MSMs) and Master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering.…
The molecular motor protein kinesin plays a key role in fundamental cellular processes such as intracellular transport, mitotic spindle formation, and cytokinesis, with important implications for neurodegenerative and cancer disease…
Molecular Dynamics (MD) simulations of proteins implicitly contain the information connecting the atomistic molecular structure and proteins' biologically relevant motion, where large-scale fluctuations are deemed to guide folding and…
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…
Kinetic theory of dissipative particle dynamics is developed in terms of a Boltzmann pair collision theory. The kinetic transport coefficients are computed from explicit collision integrals and compared favourably with detailed simulations.…
Kinetic transport models are mesoscopic mathematical descriptions of the transport of particles as well as their interactions with the background media or among themselves, and they have wide applications in many areas of mathematical…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
Euclidean distance matrices (EDMs) are a major tool for localization from distances, with applications ranging from protein structure determination to global positioning and manifold learning. They are, however, static objects which serve…
The majority of inverse kinematics (IK) algorithms search for solutions in a configuration space defined by joint angles. However, the kinematics of many robots can also be described in terms of distances between rigidly-attached points,…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
Obtaining reliable distance estimates to gas clouds within the Milky Way is challenging in the absence of certain tracers. The kinematic distance approach has been used as an alternative, derived from the assumption of circular trajectories…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Analysing stationary point databases to extract phenomenological rate constants can become time-consuming for systems with large potential energy barriers. In the present contribution we analyse several different approaches to this problem.…
We describe a systematic development of kinetic entropy as a diagnostic in fully kinetic particle-in-cell (PIC) simulations and use it to interpret plasma physics processes in heliospheric, planetary, and astrophysical systems. First, we…
We propose a mathematical kinetic framework to investigate interactions between tumor cells and the immune system, focusing on the spatial dynamics of tumor progression and immune responses. We develop two kinetic models: one describes a…
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of…