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OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics
No full textTransition path sampling techniques allow molecular dynamics simulations of complex systems to focus on rare dynamical events, providing insight into mechanisms and the ability to calculate rates inaccessible by ordinary dynamics simulations. While path sampling algorithms are conceptually as simple as importance sampling Monte Carlo, the technical complexity of their implementation has kept these techniques out of reach of the broad community. Here, we introduce an easy-to-use Python framework called OpenPathSampling (OPS) that facilitates path sampling for (bio)molecular systems with minimal effort and yet is still extensible. Interfaces to OpenMM and an internal dynamics engine for simple models are provided in the initial release, but new molecular simulation packages can easily be added. Multiple ready-to-use transition path sampling methodologies are implemented, including standard transition path sampling (TPS) between reactant and product states, transition interface sampling (TIS) and its replica exchange variant (RETIS), as well as recent multistate and multiset extensions of transition interface sampling (MSTIS, MISTIS). In addition, tools are provided to facilitate the implementation of new path sampling schemes built on basic path sampling components. In this paper, we give an overview of the design of this framework and illustrate the simplicity of applying the available path sampling algorithms to a variety of benchmark problems
Introduction to Markov state modeling with the PyEMMA software — v1.0
Get PDFThis tutorial provides an introduction to the construction of Markov models of molec- ular kinetics from molecular dynamics trajectory data with the PyEMMA software. Using tutorial notebooks, we will guide the user through the basic functionality as well as the more common advanced mechanisms. Short exercises to self check the learning progress and a notebook on troubleshooting complete this basic introduction
Efficient and reliable phase‐field simulation of brittle fracture using a nonsmooth multigrid solution scheme
No full textIn the last decades the phase‐field approach to fracture [1–3] has gained wide popularity due to advantages such as straight‐forward modeling of complex crack patterns and crack branching while allowing standard finite‐element discretizations. Time‐discrete phase‐field models of brittle fracture are typically formulated in terms of biconvex minimization problems for which a standard monolithic Newton‐Raphson scheme usually fails to converge. Solutions can be found by using operator‐splitting methods [2] or predictor‐corrector schemes [4]. Such methods come at the cost of high computational efforts. Furthermore, models incorporating the thermodynamically consistent local irreversibility of the damage phase‐field contain nonsmooth terms [2]. To improve the stability and to reduce the computational costs originating from the biconvexity and the nonsmoothness of the energy functional, we employ a nonsmooth multigrid method that can solve such problems roughly in the time of one equivalent linear problem [5] and which has been shown to be globally convergent [5]. We will demonstrate the computational speed of the proposed solution scheme by means of a classical benchmark problem of brittle fracture
Tensor-based dynamic mode decomposition
No full textDynamic mode decomposition (DMD) is a recently developed tool for the analysis of the behavior of complex dynamical systems. In this paper, we will propose an extension of DMD that exploits low-rank tensor decompositions of potentially high-dimensional data sets to compute the corresponding DMD modes and eigenvalues. The goal is to reduce the computational complexity and also the amount of memory required to store the data in order to mitigate the curse of dimensionality. The efficiency of these tensor-based methods will be illustrated with the aid of several different fluid dynamics problems such as the von Kármán vortex street and the simulation of two merging vortices
Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique
Get PDFWe employ the Grand Canonical Adaptive Resolution Molecular Dynamics Technique (GC-AdResS) to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level, thus if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably {reproduced} thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other {researchers} and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids
A 1D Multi-Tube Code for the Shockless Explosion Combustion
No full textShockless explosion combustion (SEC) has been suggested by Bobusch et al., CST, 186, 2014, as a new approach towards approximate constant volume combustion for gas turbine applications. The SEC process relies on nearly homogeneous autoignition in a premixed fuel-oxidizer charge and acoustic resonances for cyclic recharge. Operation of a single SEC tube has proven to be rather robust in numerical simulations, provided the flow control assures nearly homogeneous autoignition. Configurations with multiple tubes that fire into a common collector plenum preceding the turbine will be needed, however, to avoid excessive fluctuating thermal and mechanical load on the turbine blades. In such a configuration, the resonating tubes will interact with the volume of the plenum, and proper control of these interactions will be an important part of the engine design process. The present work presents an efficient, rough design tool that simulates the firing of such multi-tube SEC configurations into a torus-shaped turbine plenum. Both the tubes and the plenum are represented by computational quasi-one-dimensional gasdynamics modules implemented in a finite volume code for the reactive Euler equations. Suitable tube-to-plenum coupling conditions based on mass, energy, and plenum-axial momentum conservation represent the gasdynamic interactions of all engine components. First investigations utilising this tool reveal considerable dependence of the SEC-tubes’ operating conditions on the tube radius and length, and on the tubes’ positioning along the plenum torus. The SEC is especially sensitive to the plenum’s radius. Misfiring of one of the tubes does essentially not affect the operation of the others and does not even necessarily lead to a shut-down of the disturbed SEC tube
In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV - 1 genomic RNA production and packaging
No full textNanoscale domains in Ionic Liquids: A statistical mechanics definition for molecular dynamics studies
No full textOne of the many open questions concerning Ionic Liquids (ILs) is the existence of nanoscale supra-molecular domains which characterize the bulk. The hypothesis of their existence does not meet a general consensus since their definition seems to be based on ad hoc arbitrary criteria rather than on general and solid first principles of physics. In this work, we propose a suitable definition of supra-molecular domains based on first principles of statistical mechanics. Such principles can be realized through the application of a recently developed computational tool which employs adaptive molecular resolution. The method can identify the smallest region of a liquid for which the atomistic details are strictly required, while the exterior plays the role of a generic structureless thermodynamic reservoir. We consider four different imidazolium-based ILs and show that indeed one can quantitatively represent the liquid as a collection of atomistically self-contained nanodroplets embedded in a generic thermodynamic bath. Such nanodroplets express a characteristic length scale for heterogeneity in ILs
A scalable approach to the computation of invariant measures for high-dimensional Markovian systems
Get PDFThe Markovian invariant measure is a central concept in many disciplines. Conventional numerical techniques for data-driven computation of invariant measures rely on estimation and further numerical processing of a transition matrix. Here we show how the quality of data-driven estimation of a transition matrix crucially depends on the validity of the statistical independence
assumption for transition probabilities. Moreover, the cost of the invariant measure computation in general scales cubically with the dimension - and is usually unfeasible for realistic highdimensional systems. We introduce a method relaxing the independence assumption of transition probabilities that scales quadratically in situations with latent variables. Applications of the method are illustrated on the Lorenz-63 system and for the molecular dynamics (MD) simulation data of the alpha-synuclein protein. We demonstrate how the conventional methodologies do not provide good estimates of the invariant measure based upon the available alpha-synuklein MD data. Applying the introduced approach to these MD data we detect two robust meta-stable states of alpha-synuclein and a linear transition between them, involving transient formation of secondary structure, qualitatively consistent with previous purely experimental reports
The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculation
Get PDFWe have combined infrared (IR) experiments with molecular dynamics (MD)
simulations in solution at finite temperature to analyse the vibrational signature
of the small floppy peptide Alanine-Leucine. IR spectra computed from first-
principles MD simulations exhibit no distinct differences between conformational
clusters of alpha-helix/beta-sheet-like folds with different orientations of the bulky leucine
side chain. All computed spectra show two prominent bands, in good agreement
with the experiment, that are assigned to the stretch vibrations of the carbonyl
and carboxyl group, respectively. Variations in band widths and exact maxima
are likely due to small fluctuations in the backbone torsion angles