24,205 research outputs found
WavePacket: A Matlab package for numerical quantum dynamics. III: Quantum-classical simulations and surface hopping trajectories
WavePacket is an open-source program package for numerical simulations in
quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213,
223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt
with quantum dynamics of closed and open systems, respectively, the present
Part III adds fully classical and mixed quantum-classical propagations to
WavePacket. In those simulations classical phase-space densities are sampled by
trajectories which follow (diabatic or adiabatic) potential energy surfaces. In
the vicinity of (genuine or avoided) intersections of those surfaces
trajectories may switch between surfaces. To model these transitions, two
classes of stochastic algorithms have been implemented: (1) J. C. Tully's
fewest switches surface hopping and (2) Landau-Zener based single switch
surface hopping. The latter one offers the advantage of being based on
adiabatic energy gaps only, thus not requiring non-adiabatic coupling
information any more.
The present work describes the MATLAB version of WavePacket 6.0.2 which is
essentially an object-oriented rewrite of previous versions, allowing to
perform fully classical, quantum-classical and quantum-mechanical simulations
on an equal footing, i.e., for the same physical system described by the same
WavePacket input. The software package is hosted and further developed at the
Sourceforge platform, where also extensive Wiki-documentation as well as
numerous worked-out demonstration examples with animated graphics are
available
Transferable neural networks for enhanced sampling of protein dynamics
Variational auto-encoder frameworks have demonstrated success in reducing
complex nonlinear dynamics in molecular simulation to a single non-linear
embedding. In this work, we illustrate how this non-linear latent embedding can
be used as a collective variable for enhanced sampling, and present a simple
modification that allows us to rapidly perform sampling in multiple related
systems. We first demonstrate our method is able to describe the effects of
force field changes in capped alanine dipeptide after learning a model using
AMBER99. We further provide a simple extension to variational dynamics encoders
that allows the model to be trained in a more efficient manner on larger
systems by encoding the outputs of a linear transformation using time-structure
based independent component analysis (tICA). Using this technique, we show how
such a model trained for one protein, the WW domain, can efficiently be
transferred to perform enhanced sampling on a related mutant protein, the GTT
mutation. This method shows promise for its ability to rapidly sample related
systems using a single transferable collective variable and is generally
applicable to sets of related simulations, enabling us to probe the effects of
variation in increasingly large systems of biophysical interest.Comment: 20 pages, 10 figure
Robot introspection through learned hidden Markov models
In this paper we describe a machine learning approach for acquiring a model of a robot behaviour from raw sensor data. We are interested in automating the acquisition of behavioural models to provide a robot with an introspective capability. We assume that the behaviour of a robot in achieving a task can be modelled as a finite stochastic state transition system. Beginning with data recorded by a robot in the execution of a task, we use unsupervised learning techniques to estimate a hidden Markov model (HMM) that can be used both for predicting and explaining the behaviour of the robot in subsequent executions of the task. We demonstrate that it is feasible to automate the entire process of learning a high quality HMM from the data recorded by the robot during execution of its task.The learned HMM can be used both for monitoring and controlling the behaviour of the robot. The ultimate purpose of our work is to learn models for the full set of tasks associated with a given problem domain, and to integrate these models with a generative task planner. We want to show that these models can be used successfully in controlling the execution of a plan. However, this paper does not develop the planning and control aspects of our work, focussing instead on the learning methodology and the evaluation of a learned model. The essential property of the models we seek to construct is that the most probable trajectory through a model, given the observations made by the robot, accurately diagnoses, or explains, the behaviour that the robot actually performed when making these observations. In the work reported here we consider a navigation task. We explain the learning process, the experimental setup and the structure of the resulting learned behavioural models. We then evaluate the extent to which explanations proposed by the learned models accord with a human observer's interpretation of the behaviour exhibited by the robot in its execution of the task
CT-Mapper: Mapping Sparse Multimodal Cellular Trajectories using a Multilayer Transportation Network
Mobile phone data have recently become an attractive source of information
about mobility behavior. Since cell phone data can be captured in a passive way
for a large user population, they can be harnessed to collect well-sampled
mobility information. In this paper, we propose CT-Mapper, an unsupervised
algorithm that enables the mapping of mobile phone traces over a multimodal
transport network. One of the main strengths of CT-Mapper is its capability to
map noisy sparse cellular multimodal trajectories over a multilayer
transportation network where the layers have different physical properties and
not only to map trajectories associated with a single layer. Such a network is
modeled by a large multilayer graph in which the nodes correspond to
metro/train stations or road intersections and edges correspond to connections
between them. The mapping problem is modeled by an unsupervised HMM where the
observations correspond to sparse user mobile trajectories and the hidden
states to the multilayer graph nodes. The HMM is unsupervised as the transition
and emission probabilities are inferred using respectively the physical
transportation properties and the information on the spatial coverage of
antenna base stations. To evaluate CT-Mapper we collected cellular traces with
their corresponding GPS trajectories for a group of volunteer users in Paris
and vicinity (France). We show that CT-Mapper is able to accurately retrieve
the real cell phone user paths despite the sparsity of the observed trace
trajectories. Furthermore our transition probability model is up to 20% more
accurate than other naive models.Comment: Under revision in Computer Communication Journa
On the Inability of Markov Models to Capture Criticality in Human Mobility
We examine the non-Markovian nature of human mobility by exposing the
inability of Markov models to capture criticality in human mobility. In
particular, the assumed Markovian nature of mobility was used to establish a
theoretical upper bound on the predictability of human mobility (expressed as a
minimum error probability limit), based on temporally correlated entropy. Since
its inception, this bound has been widely used and empirically validated using
Markov chains. We show that recurrent-neural architectures can achieve
significantly higher predictability, surpassing this widely used upper bound.
In order to explain this anomaly, we shed light on several underlying
assumptions in previous research works that has resulted in this bias. By
evaluating the mobility predictability on real-world datasets, we show that
human mobility exhibits scale-invariant long-range correlations, bearing
similarity to a power-law decay. This is in contrast to the initial assumption
that human mobility follows an exponential decay. This assumption of
exponential decay coupled with Lempel-Ziv compression in computing Fano's
inequality has led to an inaccurate estimation of the predictability upper
bound. We show that this approach inflates the entropy, consequently lowering
the upper bound on human mobility predictability. We finally highlight that
this approach tends to overlook long-range correlations in human mobility. This
explains why recurrent-neural architectures that are designed to handle
long-range structural correlations surpass the previously computed upper bound
on mobility predictability
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