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  1. Article ; Online: Quantum scrambling across an energy barrier.

    Wolynes, Peter G / Gruebele, Martin

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 52, Page(s) e2319705120

    Language English
    Publishing date 2023-12-18
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2319705120
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  2. Article ; Online: Time-Resolved In Situ AFM Measurement of Growth Rates of Aβ40 Fibrils.

    Vekilov, Peter G / Wolynes, Peter G

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2551, Page(s) 63–77

    Abstract: We employ time-resolved in situ atomic force microcopy to monitor the growth of individual Aβ40 fibrils and thereby directly measure the fibril growth rates. We describe procedures to express and purify the Aβ peptide and verify its identity, prepare ... ...

    Abstract We employ time-resolved in situ atomic force microcopy to monitor the growth of individual Aβ40 fibrils and thereby directly measure the fibril growth rates. We describe procedures to express and purify the Aβ peptide and verify its identity, prepare solutions and seeds, quantify the displacements of the growing tips of individual fibrils, and determine their respective growth rates. We discuss approaches to evaluate and minimize the impact of the scanning tip on the monitored processes. We use the distribution of fibril thickness to characterize approximately the fibril structure. The ability to quantify faithfully the growth kinetics of amyloid fibrils empowers exploration of the molecular-level processes of fibril growth that relate to behaviors of amyloid species of laboratory and clinical interest.
    MeSH term(s) Amyloid beta-Peptides/chemistry ; Amyloid/chemistry ; Kinetics ; Peptide Fragments/chemistry
    Chemical Substances Amyloid beta-Peptides ; Amyloid ; Peptide Fragments
    Language English
    Publishing date 2022-10-29
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2597-2_6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Quantum information scrambling and chemical reactions.

    Zhang, Chenghao / Kundu, Sohang / Makri, Nancy / Gruebele, Martin / Wolynes, Peter G

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 15, Page(s) e2321668121

    Abstract: The ultimate regularity of quantum mechanics creates a tension with the assumption of classical chaos used in many of our pictures of chemical reaction dynamics. Out-of-time-order correlators (OTOCs) provide a quantum analog to the Lyapunov exponents ... ...

    Abstract The ultimate regularity of quantum mechanics creates a tension with the assumption of classical chaos used in many of our pictures of chemical reaction dynamics. Out-of-time-order correlators (OTOCs) provide a quantum analog to the Lyapunov exponents that characterize classical chaotic motion. Maldacena, Shenker, and Stanford have suggested a fundamental quantum bound for the rate of information scrambling, which resembles a limit suggested by Herzfeld for chemical reaction rates. Here, we use OTOCs to study model reactions based on a double-well reaction coordinate coupled to anharmonic oscillators or to a continuum oscillator bath. Upon cooling, as one enters the tunneling regime where the reaction rate does not strongly depend on temperature, the quantum Lyapunov exponent can approach the scrambling bound and the effective reaction rate obtained from a population correlation function can approach the Herzfeld limit on reaction rates: Tunneling increases scrambling by expanding the state space available to the system. The coupling of a dissipative continuum bath to the reaction coordinate reduces the scrambling rate obtained from the early-time OTOC, thus making the scrambling bound harder to reach, in the same way that friction is known to lower the temperature at which thermally activated barrier crossing goes over to the low-temperature activationless tunneling regime. Thus, chemical reactions entering the tunneling regime can be information scramblers as powerful as the black holes to which the quantum Lyapunov exponent bound has usually been applied.
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2321668121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  4. Article ; Online: Surface crossing and energy flow in many-dimensional quantum systems.

    Zhang, Chenghao / Gruebele, Martin / Logan, David E / Wolynes, Peter G

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 9, Page(s) e2221690120

    Abstract: ... A generalization of the Logan-Wolynes theory of quantum energy flow in many-dimensional Fermi resonance systems ...

    Abstract Energy flow in molecules, like the dynamics of other many-dimensional finite systems, involves quantum transport across a dense network of near-resonant states. For molecules in their electronic ground state, the network is ordinarily provided by anharmonic vibrational Fermi resonances. Surface crossing between different electronic states provides another route to chaotic motion and energy redistribution. We show that nonadiabatic coupling between electronic energy surfaces facilitates vibrational energy flow and, conversely, anharmonic vibrational couplings facilitate nonadiabatic electronic state mixing. A generalization of the Logan-Wolynes theory of quantum energy flow in many-dimensional Fermi resonance systems to the two-surface case gives a phase diagram describing the boundary between localized quantum dynamics and global energy flow. We explore these predictions and test them using a model inspired by the problem of electronic excitation energy transfer in the photosynthetic reaction center. Using an explicit numerical solution of the time-dependent Schrödinger equation for this ten-dimensional model, we find quite good agreement with the expectations from the approximate analytical theory.
    Language English
    Publishing date 2023-02-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2221690120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Exploring the Interplay between Disordered and Ordered Oligomer Channels on the Aggregation Energy Landscapes of α-Synuclein.

    Chen, Xun / Chen, Mingchen / Wolynes, Peter G

    The journal of physical chemistry. B

    2022  Volume 126, Issue 28, Page(s) 5250–5261

    Abstract: The abnormal aggregation of α-synulcein is associated with multiple neurodegenerative diseases such as Parkinson's disease. The hydrophobic non-amyloid component (NAC) region of α-synuclein comprises the core of the fibril in vitro and in vivo. In this ... ...

    Abstract The abnormal aggregation of α-synulcein is associated with multiple neurodegenerative diseases such as Parkinson's disease. The hydrophobic non-amyloid component (NAC) region of α-synuclein comprises the core of the fibril in vitro and in vivo. In this work, we study the aggregation landscape of the hydrophobic NAC region of α-synuclein using a transferrable coarse-grained force field, the associative memory water-mediated structure, and energy model (AWSEM). Using structural similarity, we can group metastable states on the free energy landscape of aggregation into three types of oligomers: disordered oligomers, prefibrillar oligomers with disordered tips, and ordered prefibrillar oligomers. The prefibrillar oligomers with disordered tips have more in-register parallel β strands than do the fully disordered oligomers but have fewer in-register parallel β strands than the ordered prefibrillar oligomers. Along with the ordered prefibrillar species, the disordered oligomeric states dominate at small oligomer sizes while the prefibrillar species with disordered tips thermodynamically dominate with the growth of oligomers. The topology of the aggregation landscape and observations in simulations suggest there is backtracking between ordered prefibrillar oligomers and other kinds of oligomers as the aggregation proceeds. The significant structural differences between the ordered prefibrillar oligomers and the disordered oligomers support the idea that the growth of these two kinds of oligomers involves kinetically independent parallel pathways. In contrast, the overall structural similarity between the fully ordered prefibrillar oligomers and the prefibrillar oligomers with disordered tips implies that two channels can interconvert on slower time scales. We also evaluate the effects of phosphorylation on the aggregation free energy landscape using statistical mechanical perturbation theory.
    MeSH term(s) Amyloid/chemistry ; Amyloidogenic Proteins ; Hydrophobic and Hydrophilic Interactions ; Protein Conformation, beta-Strand ; alpha-Synuclein/chemistry
    Chemical Substances Amyloid ; Amyloidogenic Proteins ; alpha-Synuclein
    Language English
    Publishing date 2022-07-10
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.2c03676
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  6. Article ; Online: The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout.

    Chen, Xun / Tsai, Min-Yeh / Wolynes, Peter G

    Journal of the American Chemical Society

    2022  Volume 144, Issue 4, Page(s) 1835–1845

    Abstract: The accurate reading of genetic information during transcription is essential for the expression of genes. Sequence binding specificity very often is attributed to short-range, usually specific interactions between amino acid residues and individual ... ...

    Abstract The accurate reading of genetic information during transcription is essential for the expression of genes. Sequence binding specificity very often is attributed to short-range, usually specific interactions between amino acid residues and individual nucleotide bases through hydrogen bonding or hydrophobic contacts: "base readout" (direct readout). In contrast, many proteins recognize DNA sequences in an alternative fashion via "shape readout" (indirect readout), where many elements of the DNA sequence cooperate to localize the transcription factor. In this study, we use a coarse-grained protein-DNA model to investigate the origin of the sequence specificity of the protein PU.1 binding to its binding sites for a series of DNA sequences. We find that the binding specificity of PU.1 is achieved primarily via a nonspecific electrostatically driven DNA mechanism involving the change in the elastic properties of the DNA. To understand the underlying mechanism, we analyze how the mechanical properties of DNA change in relation to the location of the PU.1 bound along DNA. The simulations first show that electrostatic interactions between PU.1 and DNA can cause complex DNA conformational/dynamics changes. Using a semiflexible polymer theory, we find that PU.1 influences the DNA dynamics through a second-order mechanical effect. When PU.1 binds nonspecifically to the DNA via electrostatics, the DNA becomes stiffer and the protein slides along DNA in a search mode. In contrast, once the protein finds its specific binding site, the DNA becomes softer there. PU.1 thus locks into place through configurational entropy effects, which we suggest is a generic mechanism for indirect readout.
    MeSH term(s) Base Sequence ; Binding Sites ; DNA/chemistry ; DNA/metabolism ; Elasticity ; Nucleic Acid Conformation ; Protein Binding ; Proto-Oncogene Proteins/chemistry ; Proto-Oncogene Proteins/metabolism ; Static Electricity ; Thermodynamics ; Trans-Activators/chemistry ; Trans-Activators/metabolism
    Chemical Substances Proto-Oncogene Proteins ; Trans-Activators ; proto-oncogene protein Spi-1 ; DNA (9007-49-2)
    Language English
    Publishing date 2022-01-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.1c11911
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    In stock of ZB MED Bonn / Germany

    Z 4' 55/32: Show issues
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  7. Article ; Online: Photon Activation of Glassy Dynamics: A Mechanism for Photoinduced Fluidization, Aging, and Information Storage in Amorphous Materials.

    Lubchenko, Vassiliy / Wolynes, Peter G

    The journal of physical chemistry. B

    2020  Volume 124, Issue 38, Page(s) 8434–8453

    Abstract: We discuss the photon activation of structural relaxations in glassy melts and frozen glasses containing molecules that can photoisomerize. The built-in stress following a photoinduced electronic transition lowers the thermal activation barrier for ... ...

    Abstract We discuss the photon activation of structural relaxations in glassy melts and frozen glasses containing molecules that can photoisomerize. The built-in stress following a photoinduced electronic transition lowers the thermal activation barrier for subsequent structural reconfiguration of the glassy matrix. We provide explicit predictions for the barrier distribution and structural relaxation spectrum as functions of the concentration of photoactivated molecules and the fragility of the material. The typical barrier decreases upon photoactivation, while the barrier distribution increases in width with increasing mole fraction of photoactive molecules and fluence, and becomes multimodal. In a frozen glass, the initial effects of photoisomerization locally facilitate the dynamics near the excited chromophores and can lead to complete fluidization at a sufficiently high fluence. Photon activation initially decreases the yield strength of the glass. Depending on the precise time course of illumination, there however emerges a spatial coexistence of softened regions with regions that, after being destabilized by illumination, have reconfigured so that they are now made of ultrastable glass or have crystallized as in a porcelain. This sequence of events, after illumination, can lead to highly stable amorphous solids, potentially approaching the Kauzmann limit. These mechanisms are at the root of optical information storage technologies in amorphous materials.
    Language English
    Publishing date 2020-09-15
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.0c06515
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  8. Article: Entropy Crises in Glasses and Random Heteropolymers.

    Wolynes, Peter G

    Journal of research of the National Institute of Standards and Technology

    2016  Volume 102, Issue 2, Page(s) 187–194

    Abstract: The concept of random first order transitions with configurational entropy crises provides a theoretical framework for understanding the glass transition. This paper discusses such transitions in exactly solvable spin glass models and in globular random ... ...

    Abstract The concept of random first order transitions with configurational entropy crises provides a theoretical framework for understanding the glass transition. This paper discusses such transitions in exactly solvable spin glass models and in globular random heteropolymers and their relation to glass transitions in molecular fluids and polymers. The Vogel-Fulcher law is shown to be related to the search time through the energy landscape of an "entropic droplet."
    Language English
    Publishing date 2016-10-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1473724-3
    ISSN 1044-677X ; 0160-1741
    ISSN 1044-677X ; 0160-1741
    DOI 10.6028/jres.102.014
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  9. Article ; Online: The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor.

    Chen, Xun / Jin, Shikai / Chen, Mingchen / Bueno, Carlos / Wolynes, Peter G

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 6, Page(s) e2216906120

    Abstract: The human estrogen ... ...

    Abstract The human estrogen receptor
    MeSH term(s) Humans ; Receptors, Estrogen/genetics ; Receptors, Estrogen/metabolism ; Estrogen Receptor alpha/genetics ; Estrogen Receptor alpha/metabolism ; Ligands ; Binding Sites ; DNA/metabolism ; Communication ; Protein Binding
    Chemical Substances Receptors, Estrogen ; Estrogen Receptor alpha ; Ligands ; DNA (9007-49-2)
    Language English
    Publishing date 2023-02-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2216906120
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  10. Article: Editorial: Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events.

    Trovato, Fabio / Trylska, Joanna / Bond, Peter J / Wolynes, Peter G

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 797754

    Language English
    Publishing date 2021-11-19
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.797754
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