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Johan Nilsson

Publications and source records attributed to Johan Nilsson.

At least 19 recordsLinked to original sources

Translation of Black-Box Clinical Prediction Models into Standalone Transparent Nomograms: Temporal External Validation in Heart Transplantation

We convert black-box clinical prediction models for tabular data into standalone nomograms that can be audited term by term. PRiSM (Partial Responses in Structured Models) takes the shape of each effect and interaction from the source model, not merely which variables mattered, and lets the outcome select and weight them. We tested this in 50,356 heart transplant recipients, with validation in a later era than training. Nomograms from all 5 source models - a public clinical risk score, logistic regression, neural networks, random forests and extreme gradient boosting - met a prespecified noninferiority criterion for discrimination before any further simplification, and generally preserved calibration and clinical net benefit. Those from the 3 machine-learning models showed no detectable difference in discrimination from de novo generalized additive and explainable boosting models, exceeded neural additive models, and carried fewer terms than the explainable boosting model. PRiSM is released as an open-source Python package.

cs.LG

0.82 um 105 W diode-pumped thulium-doped all silica fiber laser

An all-silica-fiber thulium-doped fiber laser emitting at 0.82 um on the transition from 3H4 to the ground state 3H6 outputs 105 W continuous-wave (CW) power and 555 W quasi-continuous-wave (QCW) instantaneous power with 0.96% duty cycle in 240-us rectangular pulses. The TDFL comprises a double-clad thulium-doped fiber (TDF) which is designed and fabricated in-house and is incorporated into an all-fiber cavity and cladding-pumped by five pigtailed diode lasers at 0.79 um. Co-lasing at 1.9 um counteracts population trapping in 3F4. The slope efficiency relative to absorbed pump power reaches 64% QCW and 77.5% CW. QCW, the beam quality M2 becomes 2.2 (beam parameter product BPP 0.57 mm mrad) and 2.45 (BPP 0.64) in orthogonal directions at ~250 W of instantaneous output power. Additionally, a modified QCW setup is continuously wavelength-tunable from 812 nm to 835 nm. We believe this is the first reported demonstration of high-power laser operation of the 3H4 to 3H6 transition in a TDF. Given also the simplicity and other attractions of an all-silica-fiber laser with direct-diode cladding-pumping, we believe our demonstration is valuable for applications ranging from laser machining of aluminum (benefitting from an absorption peak at 0.83 um) to scientific applications including strontium-based atomic clocks and cesium-based quantum metrology.

physics.optics

Quasi-continuous-wave-pumped thulium-doped fiber laser with 0.2 kW of instantaneous output power

A thulium-doped fiber laser operating quasi-continuous-wave generated 198 W of instantaneous output power in 0.2-ms pulses at 50 Hz repetition rate. The duty cycle becomes 1% and the average output power 2.0 W. This was cladding-pumped with 408 W from 0.79-um diode lasers (average pump power 4.1 W). The pump switch-on time was ~10 us at full power, with the laser exhibiting relaxation oscillations starting ~5 us after the start of the pumping and lasting for ~5 us. The slope efficiency with respect to absorbed pump power was 67% up to 200 W of absorbed pump power and 52% at the full 352 W of absorbed pump power. The low duty cycle simplified the heatsinking, despite the high instantaneous power and thermal load.

physics.optics

A Highly Efficient Hybrid Fiber Optic Laser Using a Cesium Atom Vapor Cell as an Optical Gain Medium

A new scheme of a highly efficient hybrid laser cavity is proposed and experimentally demonstrated utilizing a hot cesium (Cs) vapor cell as an optical gain medium. The laser cavity consists of a macroscopic concave reflecting mirror (>99% reflectivity) and a 4% Fresnel-reflecting perpendicularly cleaved facet of a single mode fiber (SMF). The cylindrical cesium gain cell is located between these two reflectors. The SMF serves multiple roles: 1) a passive mode-matching component to approximate the pump beam diameter to that of the laser cavity mode within the cesium cell, 2) an output coupler with low reflectivity, and 3) a high beam-quality laser delivery with a low loss. Optimizing the pump beam waist diameter and the cesium vapor cell temperature, a high slope efficiency of 86% and continuous wave power of 419 mW were obtained in the pump power range of 400 to 600 mW, with an optical-to-optical conversion efficiency of 71%. The unique multi-functional role of the SMF in the hybrid cavity is fully described, and it can also be applied to other phases of high optical gain media.

physics.optics

Ultrashort Pulse Generation in Modeless Laser Cavity

We demonstrate experimentally that random phase modulation of an erbium-doped fiber ring-laser by an intra-cavity electro-optic phase modulator did not inhibit ultrashort-pulse operation. Stable and self-starting ultrashort-pulse operation with a single pulse circulating in the cavity was achieved even when the phase modulator was driven with random sequences sufficiently fast and strong to render the laser cavity modeless, in the sense that heterodyning of the laser output did not show any spectral lines corresponding to a mode spectrum. No significant change in measured pulse characteristics was observed, compared to conventional mode-locking in the unmodulated cavity. The insensitivity to the random phase modulation is expected, given the lack of phase-sensitive elements in the cavity.

physics.optics

Single Step Phase Optimisation for Coherent Beam Combination using Deep Learning

Coherent beam combination of multiple fibres can be used to overcome limitations such as the power handling capability of single fibre configurations. In such a scheme, the focal intensity profile is critically dependent upon the relative phase of each fibre and so precise control over the phase of each fibre channel is essential. Determining the required phase compensations from the focal intensity profile alone (as measured via a camera) is extremely challenging with a large number of fibres as the phase information is obfuscated. Whilst iterative methods exist for phase retrieval, in practice, due to phase noise within a fibre laser amplification system, a single step process with computational time on the scale of milliseconds is needed. Here, we show how a neural network can be used to identify the phases of each fibre from the focal intensity profile, in a single step of ~ 10 milliseconds, for a simulated 3-ring hexagonal close packed arrangement, containing 19 separate fibres and subsequently how this enables bespoke beam shaping. In addition, we show that deep learning can be used to determine whether a desired intensity profile is physically possible within the simulation. This, coupled with the demonstrated resilience against simulated experimental noise, indicates a strong potential for the application of deep learning for coherent beam combination.

eess.IV

Equation of motion truncation scheme based on partial orthogonalization

We introduce a general scheme to consistently truncate equations of motion for Green's functions. Our scheme is guaranteed to generate physical Green's functions with real excitation energies and positive spectral weights. There are free parameters in our scheme akin to mean field parameters that may be determined to get as good an approximation to the physics as possible. As a test case we apply our scheme to a two-pole approximation for the 2D Hubbard model. At half-filling we find an insulating solution with several interesting properties: it has low expectation value of the energy and it gives upper and lower Hubbard bands with the full non-interacting bandwidth in the large U limit. Away from half-filling, in particular in the intermediate interaction regime, our scheme allows for several different phases with different number of Fermi surfaces and topologies.

cond-mat.str-el

Efficient extraction of high pulse energy from partly quenched highly Er3+-doped fiber amplifiers

We demonstrate efficient pulse-energy extraction from a partly-quenched erbium-doped aluminosilicate fiber amplifier. This has a high erbium-concentration, which allows for short devices with reduced nonlinear distortions, but which also results in partial quenching and thus significant unsaturable absorption, even though the fiber is still able to amplify. Although the quenching degrades the average-power efficiency, the pulse energy remains high, and our results point to an increasingly promising outcome for short pulses. Furthermore, unlike unquenched fibers, the conversion efficiency improves at low repetition rates, which we attribute to smaller relative energy loss to quenched ions at higher pulse energy. A short (2.6 m) cladding-pumped partly-quenched Er-doped-fiber with 95-dB/m 1530-nm peak absorption and saturation energy estimated to 85 μJ, reached 0.8 mJ of output energy when seeded by 0.2-μs, 23-μJ pulses. Thus, according to our results, pulses can be amplified to high energy in short highly-Er-doped fibers designed to reduce nonlinear distortions, at the expense of average-power efficiency

physics.optics

The Hubbard dimer within the Green's function equation of motion approach

We consider a formulation of the equation of motion technique for Green's function in which the unknown averages are computed by solving a linear system. This linear system appears solvable for all finite temperatures, but depending on the system parameters the condition number can be very large, making the solution numerically unfeasible at low temperatures. In the example that we consider, the Hubbard dimer, we can get rid of this problem by making use of total spin as a good quantum number.

cond-mat.str-el

Physics-inspired derivations of some algorithms for computing the permanent

We provide physics-inspired derivations of a number of algorithms for computing the permanent of a matrix. In particular we formulate the computation of the permanent as a Grassmann integral that may be viewed as an interacting many-fermion problem. Applying a discrete Hubbard-Stratonovich decoupling then gives approximation schemes that are equivalent to the familiar determinant Monte Carlo algorithm. This leads to elementary derivations of the well-known estimators of Godsil-Gutman and Karmarkar et al. Another straightfoward manipulation of the Grassmann integral, making use of gauge invariance, gives the efficient exact formula of Glynn. In addition to these known results we also give some additional estimators and formulas that are natural in our formulation.

math-ph

Multiple scales and phases in discrete chains with application to folded proteins

Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape. Multiple scales produces also complex dynamics, which in the case of proteins sustains live matter. However, thus far no clear understanding exist, how to distinguish the various scales that determine the structure and dynamics of a complex protein. Here we propose a systematic method to identify the scales in chiral heteropolymers such as a protein. For this we introduce a novel order parameter, that not only reveals the scales but also probes the phase structure. In particular, we argue that a chiral heteropolymer can simultaneously display traits of several different phases, contingent on the length scale at which it is scrutinized. Our approach builds on a variant of Kadanoff's block-spin transformation that we employ to coarse grain piecewise linear chains such as the C$α$ backbone of a protein. We derive analytically and then verify numerically a number of properties that the order parameter can display. We demonstrate how, in the case of crystallographic protein structures in Protein Data Bank, the order parameter reveals the presence of different length scales, and we propose that a relation must exist between the scales, phases, and the complexity of folding pathways.

cond-mat.soft

Scaling of the Thue-Morse diffraction measure

We revisit the well-known and much studied Riesz product representation of the Thue-Morse diffraction measure, which is also the maximal spectral measure for the corresponding dynamical spectrum in the complement of the pure point part. The known scaling relations are summarised, and some new findings are explained.

math-ph

Non-Linear Methods in Strongly Correlated Electron Systems

We analyze the structure of the group of (local) non-linear canonical transformations that exist in a system with n fermionic modes. To perform our study we develop an alternative framework to represent the generators of these canonical transformations; indeed we show how their definition, understanding and control is significantly improved using the Majorana fermion representation. These canonical transformations have the structure of a Lie group and we provide a representation for the elements of the Lie algebra that is very convenient both conceptually and practically (computationally): indeed our framework yields as side product an extremely effective tool to handle and work with SU(2n) Lie groups and algebras. Granting an enhanced control of the group of non-linear canonical transformation, our framework can be helpful in the study of strongly correlated electron systems, since it allows to easily identify fermionic degrees of freedom able to capture part of the correlations and thus may give a simpler representation of the Hamiltonian. Thanks to our analysis, also symmetry-based studies of the quantum Hamiltonians can be improved, since the simple representation of the generators of the canonical group permits to identify and understand otherwise hidden symmetries of difficult interpretation. The main aim of this work is to provide a comprehensive, general and scrupulous analysis of this framework, that we already applied in some circumstances. Therefore specific applications will not be presented in detail, since they can be found elsewhere, while only the formal and conceptual aspects will be developed thoroughly.

cond-mat.str-el

Substitution Rules for Higher-Dimensional Paperfolding Structures

We present a general scheme how to construct a substitution rule for generating $d$-dimensional analogues of the paperfolding structures. This substitution is proven to be primitive, so that the translation action on the hull forms a strictly ergodic dynamical system. The substitution admits a coincidence in the sense of Dekking, which implies that the dynamical system has pure point spectrum. The same then holds true also for the diffraction spectrum. The substitution also allows us to give estimates on the complexity of the paperfolding structures, and to determine topological invariants like the Čech cohomology groups of the hull for dimensions $d\le2$.

math.DS

Free fermion description of a paramagnetic Mott insulator

A scheme is presented that enables a description of a paramagnetic Mott insulator in terms of free fermions. The main idea is to view the physical fermions as a part of a multi-band system and to allow for a correlation between the physical fermions and the auxiliary ones. Technically this is implemented through a non-linear canonical transformation, which is conveniently formulated in terms of Majorana fermions. The transformed Hamiltonian is in the next stage approximated with a free fermion theory. The approximation step is variational and provides an upper bound on the ground state energy at zero or the Free energy at finite temperature.

cond-mat.str-el