84 research outputs found
Fluctuation relations for systems in constant magnetic field
The validity of the Fluctuation Relations (FR) for systems in a constant
magnetic field is investigated. Recently introduced time-reversal symmetries
that hold in presence of static electric and magnetic fields and of
deterministic thermostats are used to prove the transient FR without invoking,
as commonly done, inversion of the magnetic field. Steady-state FR are also
derived, under the t-mixing condition. These results extend the predictive
power of important statistical mechanics relations. We illustrate this via the
non-linear response for the cumulants of the dissipation, showing how the new
FR enable to determine analytically null cumulants also for systems in a single
magnetic field.Comment: 1 figure, added reference
Analysis of the quantum-classical Liouville equation in the mapping basis
The quantum-classical Liouville equation provides a description of the
dynamics of a quantum subsystem coupled to a classical environment.
Representing this equation in the mapping basis leads to a continuous
description of discrete quantum states of the subsystem and may provide an
alternate route to the construction of simulation schemes. In the mapping basis
the quantum-classical Liouville equation consists of a Poisson bracket
contribution and a more complex term. By transforming the evolution equation,
term-by-term, back to the subsystem basis, the complex term (excess coupling
term) is identified as being due to a fraction of the back reaction of the
quantum subsystem on its environment. A simple approximation to
quantum-classical Liouville dynamics in the mapping basis is obtained by
retaining only the Poisson bracket contribution. This approximate mapping form
of the quantum-classical Liouville equation can be simulated easily by
Newtonian trajectories. We provide an analysis of the effects of neglecting the
presence of the excess coupling term on the expectation values of various types
of observables. Calculations are carried out on nonadiabatic population and
quantum coherence dynamics for curve crossing models. For these observables,
the effects of the excess coupling term enter indirectly in the computation and
good estimates are obtained with the simplified propagation
Approximating Time-Dependent Quantum Statistical Properties
Computing quantum dynamics in condensed matter systems is an open challenge due to the exponential scaling of exact algorithms with the number of degrees of freedom. Current methods try to reduce the cost of the calculation using classical dynamics as the key ingredient of approximations of the quantum time evolution. Two main approaches exist, quantum classical and semi-classical, but they suffer from various difficulties, in particular when trying to go beyond the classical approximation. It may then be useful to reconsider the problem focusing on statistical time-dependent averages rather than directly on the dynamics. In this paper, we discuss a recently developed scheme for calculating symmetrized correlation functions. In this scheme, the full (complex time) evolution is broken into segments alternating thermal and real-time propagation, and the latter is reduced to classical dynamics via a linearization approximation. Increasing the number of segments systematically improves the result with respect to full classical dynamics, but at a cost which is still prohibitive. If only one segment is considered, a cumulant expansion can be used to obtain a computationally efficient algorithm, which has proven accurate for condensed phase systems in moderately quantum regimes. This scheme is summarized in the second part of the paper. We conclude by outlining how the cumulant expansion formally provides a way to improve convergence also for more than one segment. Future work will focus on testing the numerical performance of this extension and, more importantly, on investigating the limit for the number of segments that goes to infinity of the approximate expression for the symmetrized correlation function to assess formally its convergence to the exact result
Fluctuation relations for dissipative systems in constant external magnetic field: theory and molecular dynamics simulations
It has recently been pointed out that Hamiltonian particle systems in
constant magnetic fields satisfy generalized time-reversal symmetries that
enable to prove useful statistical relationships based on equilibrium
phase-space probability distributions without the need to invert, as commonly
considered necessary, the magnetic field. Among these relations, that hold
without need of Casimir modifications, one finds the standard linear response
Green-Kubo relations, and consequently the Onsager reciprocal relations. Going
beyond linear response is also possible, for instance in terms of transient and
steady state Fluctuation Relations (FRs). Here we highlight how the generalized
time-reversal symmetries ensure that the (transient) FRs theory directly
applies also for systems in external magnetic fields. Furthermore we show that
transient FR can indeed be verified in nonequilibrium molecular dynamics
simulations, for systems subjected to magnetic and electric fields, which are
thermostatted \`a la Nos\'e-Hoover. The result is nontrivial because, since it
is not immediate within which sizes and time scales the effects can actually be
observable, it is not obvious what one may obtain by real molecular dynamics
simulations.Comment: Submitted to Entropy, 17 pages, 4 figures, 1 tabl
Jupyter widgets and extensions for education and research in computational physics and chemistry
Python and Jupyter are becoming increasingly popular tools for computational
physics and chemistry research and education. Interactive notebooks are a
precious tool for creating graphical user interfaces and teaching materials,
and Jupyter widgets constitute the core of their interactive functionality.
Packages and libraries which offer a broad range of widgets for general
purposes exist, but the lack of specialized widgets for computational physics,
chemistry and materials science implies significant time investments for the
development of effective Jupyter notebooks for research and education in these
domains. Here, we present custom Jupyter widgets that we have developed to
target the needs of these research and teaching communities. These widgets
constitute high quality interactive graphical components and can be employed,
for example, as tools to visualize and manipulate data, or to explore different
visual representations of concepts, illuminating the relationships existing
between them. In addition, we discuss the JupyterLab extensions that we
developed to modify the JupyterLab interface for an enhanced user experience
when working with various applications within the targeted scientific domains.Comment: 19 pages, 9 figure
SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions
Considerable importance in molecular biophysics is attached to influencing by mutagenesis the specific properties of a protein family. The working hypothesis is that mutating residues at few selected positions can affect specificity. Statistical analysis of homologue sequences can identify putative specificity determining positions (SDPs) and help to shed some light on the peculiarities underlying their functional role. In this work, we present an approach to identify such positions inspired by state of the art mutual information-based SDP prediction methods. The algorithm based on this approach provides a systematic procedure to point at the relevant physical characteristics of putative SPDs and can investigate the effects of correlated mutations. The method is tested on two standard benchmarks in the field and further validated in the context of a biologically interesting problem: the multimerization of the Intrinsically Fluorescent Proteins (IFP)
ERS International Congress 2021: highlights from the Interstitial Lung Diseases Assembly
This article provides an overview of scientific highlights in the field of interstitial lung disease (ILD), presented at the virtual European Respiratory Society Congress 2021. A broad range of topics was discussed this year, ranging from translational and genetic aspects to novel innovations with the potential to improve the patient pathway. Early Career Members summarise a selection of interesting findings from different congress sessions, together with the leadership of Assembly 12 - Interstitial Lung Disease. © The authors 2022
Integrating Clinical Probability into the Diagnostic Approach to Idiopathic Pulmonary Fibrosis: An International Working Group Perspective
Background. When considering the diagnosis of idiopathic pulmonary fibrosis (IPF), experienced
clinicians integrate clinical features that help to differentiate IPF from other fibrosing interstitial lung
diseases, thus generating a “pre-test” probability of IPF. The aim of this international working group
perspective was to summarize these features using a tabulated approach similar to chest HRCT and
histopathologic patterns reported in the international guidelines for the diagnosis of IPF, and to help
formally incorporate these clinical likelihoods into diagnostic reasoning to facilitate the diagnosis of
IPF.
Methods. The committee group identified factors that influence the clinical likelihood of a diagnosis
of IPF, which was categorized as a pre-test clinical probability of IPF into “high” (70-100%),
“intermediate” (30-70%), or “low” (0-30%). After integration of radiological and histopathological
features, the post-test probability of diagnosis was categorized into “definite” (90-100%), “high
confidence” (70-89%), “low confidence” (51-69%), or “low” (0-50%) probability of IPF.
Findings. A conceptual Bayesian framework was created, integrating the clinical likelihood of IPF
(“pre-test probability of IPF”) with the HRCT pattern, the histopathology pattern when available,
and/or the pattern of observed disease behavior into a “post-test probability of IPF”. The diagnostic
probability of IPF was expressed using an adapted diagnostic ontology for fibrotic interstitial lung
diseases.
Interpretation. The present approach will help incorporate the clinical judgement into the diagnosis
of IPF, thus facilitating the application of IPF diagnostic guidelines and, ultimately improving
diagnostic confidence and reducing the need for invasive diagnostic techniques
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