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  1. Book ; Online: Particle Polarization in High Energy Physics

    Faccioli, Pietro / Lourenço, Carlos

    An Introduction and Case Studies on Vector Particle Production at the LHC

    (Lecture Notes in Physics ; 1002)

    2023  

    Author's details by Pietro Faccioli, Carlos Lourenço
    Series title Lecture Notes in Physics ; 1002
    Keywords Elementary particles (Physics) ; Quantum field theory ; Measurement ; Measuring instruments ; Particle accelerators
    Subject code 530.14
    Language English
    Size 1 Online-Ressource (XV, 302 p. 127 illus. in color)
    Edition 1st ed. 2023
    Publisher Springer International Publishing ; Imprint: Springer
    Publishing place Cham
    Document type Book ; Online
    HBZ-ID HT021680081
    ISBN 978-3-031-08876-6 ; 9783031088742 ; 9783031088759 ; 3-031-08876-X ; 3031088743 ; 3031088751
    DOI 10.1007/978-3-031-08876-6
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book ; Online: Particle Polarization in High Energy Physics

    Faccioli, Pietro / Lourenço, Carlos

    An Introduction and Case Studies on Vector Particle Production at the LHC

    (Lecture Notes in Physics)

    2023  

    Series title Lecture Notes in Physics
    Keywords Quantum physics (quantum mechanics & quantum field theory) ; Mensuration & systems of measurement ; Particle & high-energy physics ; Angular Distributions of Particle Decays ; Angular Momentum in Experimental Hep ; Decay of Standard-model Vector Bosons ; Frame-invariant Relations ; LHC Angular Momentum ; Polarization Measurement in Hep ; Polarizazion Frames
    Language English
    Size 1 electronic resource (302 pages)
    Publisher Springer Nature
    Publishing place Cham
    Document type Book ; Online
    Note English
    HBZ-ID HT030379422
    ISBN 9783031088766 ; 303108876X
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article ; Online: Functional, pathogenic, and pharmacological roles of protein folding intermediates.

    Biasini, Emiliano / Faccioli, Pietro

    Proteins

    2023  

    Abstract: Protein expression and function in eukaryotic cells are tightly harmonized processes modulated by the combination of different layers of regulation, including transcription, processing, stability, and translation of messenger RNA, as well as assembly, ... ...

    Abstract Protein expression and function in eukaryotic cells are tightly harmonized processes modulated by the combination of different layers of regulation, including transcription, processing, stability, and translation of messenger RNA, as well as assembly, maturation, sorting, recycling, and degradation of polypeptides. Integrating all these pathways and the protein quality control machinery, deputed to avoid the production and accumulation of aberrantly folded proteins, determines protein homeostasis. Over the last decade, the combined development of accurate time-resolved experimental techniques and efficient computer simulations has opened the possibility of investigating biological mechanisms at atomic resolution with physics-based models. A meaningful example is the reconstruction of protein folding pathways at atomic resolution, which has enabled the characterization of the folding kinetics of biologically relevant globular proteins consisting of a few hundred amino acids. Combining these innovative computational technologies with rigorous experimental approaches reveals the existence of non-native metastable states transiently appearing along the folding process of such proteins. Here, we review the primary evidence indicating that these protein folding intermediates could play roles in disparate biological processes, from the posttranslational regulation of protein expression to disease-relevant protein misfolding mechanisms. Finally, we discuss how the information encoded into protein folding pathways could be exploited to design an entirely new generation of pharmacological agents capable of promoting the selective degradation of protein targets.
    Language English
    Publishing date 2023-02-13
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 806683-8
    ISSN 1097-0134 ; 0887-3585
    ISSN (online) 1097-0134
    ISSN 0887-3585
    DOI 10.1002/prot.26479
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  4. Article ; Online: Sampling a Rare Protein Transition Using Quantum Annealing.

    Ghamari, Danial / Covino, Roberto / Faccioli, Pietro

    Journal of chemical theory and computation

    2024  Volume 20, Issue 8, Page(s) 3322–3334

    Abstract: Simulating spontaneous structural rearrangements in macromolecules with classical molecular dynamics is an outstanding challenge. Conventional supercomputers can access time intervals of up to tens of μs, while many key events occur on exponentially ... ...

    Abstract Simulating spontaneous structural rearrangements in macromolecules with classical molecular dynamics is an outstanding challenge. Conventional supercomputers can access time intervals of up to tens of μs, while many key events occur on exponentially longer time scales. Path sampling techniques have the advantage of focusing the computational power on barrier-crossing trajectories, but generating uncorrelated transition paths that explore diverse conformational regions remains a problem. We employ a hybrid path-sampling paradigm that addresses this issue by generating trial transition paths using a quantum annealing (QA) machine. We first employ a classical computer to perform an uncharted exploration of the conformational space. The data set generated in this exploration is then postprocessed using a path integral-based method to yield a coarse-grained network representation of the reactive kinetics. By resorting to a quantum annealer, quantum superposition can be exploited to encode all of the transition pathways in the initial quantum state, thus potentially solving the path exploration problem. Furthermore, each QA cycle yields a completely uncorrelated trial trajectory. We previously validated this scheme on a prototypically simple transition, which could be extensively characterized on a desktop computer. Here, we scale up in complexity and perform an all-atom simulation of a protein conformational transition that occurs on the millisecond time scale, obtaining results that match those of the Anton special-purpose supercomputer. Despite limitations due to the available quantum annealers, our study highlights how realistic biomolecular simulations provide potentially impactful new ground for applying, testing, and advancing quantum technologies.
    Language English
    Publishing date 2024-04-08
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c01174
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Quantum-inspired encoding enhances stochastic sampling of soft matter systems.

    Slongo, Francesco / Hauke, Philipp / Faccioli, Pietro / Micheletti, Cristian

    Science advances

    2023  Volume 9, Issue 43, Page(s) eadi0204

    Abstract: Quantum advantage in solving physical problems is still hard to assess due to hardware limitations. However, algorithms designed for quantum computers may engender transformative frameworks for modeling and simulating paradigmatically hard systems. Here, ...

    Abstract Quantum advantage in solving physical problems is still hard to assess due to hardware limitations. However, algorithms designed for quantum computers may engender transformative frameworks for modeling and simulating paradigmatically hard systems. Here, we show that the quadratic unconstrained binary optimization encoding enables tackling classical many-body systems that are challenging for conventional Monte Carlo. Specifically, in self-assembled melts of rigid lattice ring polymers, the combination of high density, chain stiffness, and topological constraints results in divergent autocorrelation times for real-space Monte Carlo. Our quantum-inspired encoding overcomes this problem and enables sampling melts of lattice rings with fixed curvature and compactness, unveiling counterintuitive topological effects. Tackling the same problems with the D-Wave quantum annealer leads to substantial performance improvements and advantageous scaling of sampling computational cost with the size of the self-assembled ring melts.
    Language English
    Publishing date 2023-10-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adi0204
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.

    Lazzeri, Gianmarco / Micheletti, Cristian / Pasquali, Samuela / Faccioli, Pietro

    Biophysical journal

    2023  Volume 122, Issue 15, Page(s) 3089–3098

    Abstract: Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. As a step forward in ... ...

    Abstract Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. As a step forward in tackling these issues, we extend to RNA an enhanced path-sampling method previously successfully applied to proteins. In this scheme, the information about the RNA's native structure is harnessed by a soft history-dependent biasing force promoting the generation of productive folding trajectories in an all-atom force field with explicit solvent. A rigorous variational principle is then applied to minimize the effect of the bias. Here, we report on an application of this method to RNA molecules from 20 to 47 nucleotides long and increasing topological complexity. By comparison with analog simulations performed on small proteins with similar size and architecture, we show that the RNA folding landscape is significantly more frustrated, even for relatively small chains with a simple topology. The predicted RNA folding mechanisms are found to be consistent with the available experiments and some of the existing coarse-grained models. Due to its computational performance, this scheme provides a promising platform to efficiently gather atomistic RNA folding trajectories, thus retain the information about the chemical composition of the sequence.
    MeSH term(s) Protein Folding ; RNA Folding ; Proteins/chemistry ; Molecular Conformation ; RNA ; Molecular Dynamics Simulation ; Thermodynamics
    Chemical Substances Proteins ; RNA (63231-63-0)
    Language English
    Publishing date 2023-06-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2023.06.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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    Zs.MO 2: Show issues

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  7. Article ; Online: Molecular dynamics at low time resolution.

    Faccioli, P

    The Journal of chemical physics

    2010  Volume 133, Issue 16, Page(s) 164106

    Abstract: The internal dynamics of macromolecular systems is characterized by widely separated time scales, ranging from fraction of picoseconds to nanoseconds. In ordinary molecular dynamics simulations, the elementary time step Δt used to integrate the equation ... ...

    Abstract The internal dynamics of macromolecular systems is characterized by widely separated time scales, ranging from fraction of picoseconds to nanoseconds. In ordinary molecular dynamics simulations, the elementary time step Δt used to integrate the equation of motion needs to be chosen much smaller of the shortest time scale in order not to cut-off physical effects. We show that in systems obeying the overdamped Langevin equation, it is possible to systematically correct for such discretization errors. This is done by analytically averaging out the fast molecular dynamics which occurs at time scales smaller than Δt, using a renormalization group based technique. Such a procedure gives raise to a time-dependent calculable correction to the diffusion coefficient. The resulting effective Langevin equation describes by construction the same long-time dynamics, but has a lower time resolution power, hence it can be integrated using larger time steps Δt. We illustrate and validate this method by studying the diffusion of a point-particle in a one-dimensional toy model and the denaturation of a protein.
    MeSH term(s) Algorithms ; Bacterial Proteins/chemistry ; Hot Temperature ; Molecular Dynamics Simulation ; Protein Denaturation ; Proteins/chemistry ; Streptococcus/chemistry ; Time Factors
    Chemical Substances Bacterial Proteins ; IgG Fc-binding protein, Streptococcus ; Proteins
    Language English
    Publishing date 2010-10-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/1.3493459
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods.

    Röder, Konstantin / Stirnemann, Guillaume / Faccioli, Pietro / Pasquali, Samuela

    QRB discovery

    2022  Volume 3, Page(s) e21

    Abstract: While RNA folding was originally seen as a simple problem to solve, it has been shown that the promiscuous interactions of the nucleobases result in structural polymorphism, with several competing structures generally observed for non-coding RNA. This ... ...

    Abstract While RNA folding was originally seen as a simple problem to solve, it has been shown that the promiscuous interactions of the nucleobases result in structural polymorphism, with several competing structures generally observed for non-coding RNA. This inherent complexity limits our understanding of these molecules from experiments alone, and computational methods are commonly used to study RNA. Here, we discuss three advanced sampling schemes, namely Hamiltonian-replica exchange molecular dynamics (MD), ratchet-and-pawl MD and discrete path sampling, as well as the HiRE-RNA coarse-graining scheme, and highlight how these approaches are complementary with reference to recent case studies. While all computational methods have their shortcomings, the plurality of simulation methods leads to a better understanding of experimental findings and can inform and guide experimental work on RNA polymorphism.
    Language English
    Publishing date 2022-10-17
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2633-2892
    ISSN (online) 2633-2892
    DOI 10.1017/qrd.2022.19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Sampling rare conformational transitions with a quantum computer.

    Ghamari, Danial / Hauke, Philipp / Covino, Roberto / Faccioli, Pietro

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 16336

    Abstract: Structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, Molecular Dynamics (MD) simulations enable us to investigate these thermally activated processes with an atomic level of ... ...

    Abstract Structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, Molecular Dynamics (MD) simulations enable us to investigate these thermally activated processes with an atomic level of resolution. In practice, an exponentially large fraction of computational resources must be invested to simulate thermal fluctuations in metastable states. Path sampling methods focus the computational power on sampling the rare transitions between states. One of their outstanding limitations is to efficiently generate paths that visit significantly different regions of the conformational space. To overcome this issue, we introduce a new algorithm for MD simulations that integrates machine learning and quantum computing. First, using functional integral methods, we derive a rigorous low-resolution spatially coarse-grained representation of the system's dynamics, based on a small set of molecular configurations explored with machine learning. Then, we use a quantum annealer to sample the transition paths of this low-resolution theory. We provide a proof-of-concept application by simulating a benchmark conformational transition with all-atom resolution on the D-Wave quantum computer. By exploiting the unique features of quantum annealing, we generate uncorrelated trajectories at every iteration, thus addressing one of the challenges of path sampling. Once larger quantum machines will be available, the interplay between quantum and classical resources may emerge as a new paradigm of high-performance scientific computing. In this work, we provide a platform to implement this integrated scheme in the field of molecular simulations.
    MeSH term(s) Benchmarking ; Computers ; Computing Methodologies ; Molecular Conformation ; Quantum Theory
    Language English
    Publishing date 2022-09-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-20032-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Erratum: "All-atom calculation of protein free-energy profiles" [J. Chem. Phys. 147, 152724 (2017)].

    Orioli, S / Ianeselli, A / Spagnolli, G / Faccioli, P

    The Journal of chemical physics

    2019  Volume 150, Issue 5, Page(s) 59901

    Language English
    Publishing date 2019-02-02
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/1.5063534
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    In stock of ZB MED Bonn / Germany

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