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  1. Article ; Online: Colleagues of Ken A. Dill.

    Dill, Ken A

    The journal of physical chemistry. B

    2018  Volume 122, Issue 21, Page(s) 5267–5268

    Language English
    Publishing date 2018-05-30
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.8b02468
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Selected Publications of Ken A. Dill.

    Dill, Ken A

    The journal of physical chemistry. B

    2018  Volume 122, Issue 21, Page(s) 5269–5277

    Language English
    Publishing date 2018-05-30
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.8b02467
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Autobiography of Ken A. Dill.

    Dill, Ken A

    The journal of physical chemistry. B

    2018  Volume 122, Issue 21, Page(s) 5263–5266

    Language English
    Publishing date 2018-05-30
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.8b02469
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Computational Procedure for Predicting Excipient Effects on Protein-Protein Affinities.

    Dignon, Gregory L / Dill, Ken A

    Journal of chemical theory and computation

    2024  Volume 20, Issue 3, Page(s) 1479–1488

    Abstract: Protein-protein interactions lie at the center of many biological processes and are a challenge in formulating biological drugs, such as antibodies. A key to mitigating protein association is to use small-molecule additives, i.e., excipients that can ... ...

    Abstract Protein-protein interactions lie at the center of many biological processes and are a challenge in formulating biological drugs, such as antibodies. A key to mitigating protein association is to use small-molecule additives, i.e., excipients that can weaken protein-protein interactions. Here, we develop a computationally efficient model for predicting the viscosity-reducing effect of different excipient molecules by combining atomic-resolution MD simulations, binding polynomials, and a thermodynamic perturbation theory. In a proof of principle, this method successfully ranks the order of four types of excipients known to reduce the viscosity of solutions of a particular monoclonal antibody. This approach appears useful for predicting the effects of excipients on protein association and phase separation, as well as the effects of buffers on protein solutions.
    MeSH term(s) Excipients/chemistry ; Antibodies, Monoclonal/chemistry ; Viscosity
    Chemical Substances Excipients ; Antibodies, Monoclonal
    Language English
    Publishing date 2024-01-31
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c01197
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Next-Gen Biophysics: Look to the Forest, Beyond the Trees.

    Schmit, Jeremy / Dill, Ken A

    Annual review of biophysics

    2023  Volume 52, Page(s) v–viii

    MeSH term(s) Trees ; Forests
    Language English
    Publishing date 2023-05-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2434725-5
    ISSN 1936-1238 ; 1936-122X
    ISSN (online) 1936-1238
    ISSN 1936-122X
    DOI 10.1146/annurev-bb-52-030923-100001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Se 190: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Origins of life: first came evolutionary dynamics.

    Kocher, Charles / Dill, Ken A

    QRB discovery

    2023  Volume 4, Page(s) e4

    Abstract: When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than seeking ... ...

    Abstract When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than seeking a
    Language English
    Publishing date 2023-03-22
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2633-2892
    ISSN (online) 2633-2892
    DOI 10.1017/qrd.2023.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: A computational procedure for predicting excipient effects on protein-protein affinities.

    Dignon, Gregory L / Dill, Ken A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Protein-protein interactions lie at the center of much biology and are a challenge in formulating biological drugs such as antibodies. A key to mitigating protein association is to use small molecule additives, i.e. excipients that can weaken protein- ... ...

    Abstract Protein-protein interactions lie at the center of much biology and are a challenge in formulating biological drugs such as antibodies. A key to mitigating protein association is to use small molecule additives, i.e. excipients that can weaken protein-protein interactions. Here, we develop a computationally efficient model for predicting the viscosity-reducing effect of different excipient molecules by combining atomic-resolution MD simulations, binding polynomials and a thermodynamic perturbation theory. In a proof of principle, this method successfully rank orders four types of excipients known to reduce the viscosity of solutions of a particular monoclonal antibody. This approach appears useful for predicting effects of excipients on protein association and phase separation, as well as the effects of buffers on protein solutions.
    Language English
    Publishing date 2023-12-23
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.22.573113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Nonequilibrium statistical physics beyond the ideal heat bath approximation.

    Pachter, Jonathan Asher / Dill, Ken A

    Physical review. E

    2023  Volume 107, Issue 1-1, Page(s) 14131

    Abstract: Important models of nonequilibrium statistical physics (NESP) are limited by a commonly used, but often unrecognized, near-equilibrium approximation. Fokker-Planck and Langevin equations, the Einstein and random-flight diffusion models, and the ... ...

    Abstract Important models of nonequilibrium statistical physics (NESP) are limited by a commonly used, but often unrecognized, near-equilibrium approximation. Fokker-Planck and Langevin equations, the Einstein and random-flight diffusion models, and the Schnakenberg model of biochemical networks suppose that fluctuations are due to an ideal equilibrium bath. But far from equilibrium, this perfect bath concept does not hold. A more principled approach should derive the rate fluctuations from an underlying dynamical model, rather than assuming a particular form. Here, using maximum caliber as the underlying principle, we derive corrections for NESP processes in an imperfect-but more realistic-environment, corrections which become particularly important for a system driven strongly away from equilibrium. Beyond characterizing a heat bath by the single equilibrium property of its temperature, the bath's speed and size must also be used to characterize the bath's ability to handle fast or large fluctuations.
    Language English
    Publishing date 2023-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.107.014131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Darwinian evolution as a dynamical principle.

    Kocher, Charles D / Dill, Ken A

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

    2023  Volume 120, Issue 11, Page(s) e2218390120

    Abstract: Darwinian evolution (DE)-biology's powerful process of adaptation-is remarkably different from other known dynamical processes. It is antithermodynamic, driving away from equilibrium; it has persisted for 3.5 billion years; and its target, fitness, can ... ...

    Abstract Darwinian evolution (DE)-biology's powerful process of adaptation-is remarkably different from other known dynamical processes. It is antithermodynamic, driving away from equilibrium; it has persisted for 3.5 billion years; and its target, fitness, can seem like "Just So" stories. For insights, we make a computational model. In the Darwinian Evolution Machine (DEM) model, resource-driven duplication and competition operate inside a cycle of search/compete/choose. We find the following: 1) DE requires multiorganism coexistence for its long-term persistence and ability to cross fitness valleys. 2) DE is driven by resource dynamics, like booms and busts, not just by mutational change. And, 3) fitness ratcheting requires a mechanistic separation between variation and selection steps, perhaps explaining biology's use of separate polymers, DNA and proteins.
    Language English
    Publishing date 2023-03-07
    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.2218390120
    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)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: Simple Model of Liquid Water Dynamics.

    Urbic, Tomaz / Dill, Ken A

    The journal of physical chemistry. B

    2023  Volume 127, Issue 37, Page(s) 7996–8001

    Abstract: We develop an analytical statistical-mechanical model to study the dynamic properties of liquid water. In this two-dimensional model, neighboring waters can interact through a hydrogen bond, a van der Waals contact, or an ice-like cage structure or have ... ...

    Abstract We develop an analytical statistical-mechanical model to study the dynamic properties of liquid water. In this two-dimensional model, neighboring waters can interact through a hydrogen bond, a van der Waals contact, or an ice-like cage structure or have no interaction. We calculate the diffusion coefficient, viscosity, and thermal conductivity versus temperature and pressure. The trends follow those seen in the water experiments. The model explains that in warm water, heating drives faster diffusion but less interaction, so the viscosity and conductivity decrease. Cooling cold water causes poorer energy exchange because water's ice-like cages are big and immobile and collide infrequently. The main antagonism in water dynamics is not between vdW and H bonds, but it is an interplay between both those pair interactions, multibody cages, and no interaction. The value of this simple model is that it is analytical, so calculations are immediate, and it gives interpretations based on molecular physics.
    Language English
    Publishing date 2023-09-06
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c05212
    Database MEDical Literature Analysis and Retrieval System OnLINE

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