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  1. Artikel ; Online: Specialization at an expanding front.

    Li, Lauren H / Kardar, Mehran

    Physical review. E

    2023  Band 108, Heft 3, Seite(n) L032402

    Abstract: As a population grows, spreading to new environments may favor specialization. In this paper, we introduce and explore a model for specialization at the front of a colony expanding synchronously into new territory. We show through numerical simulations ... ...

    Abstract As a population grows, spreading to new environments may favor specialization. In this paper, we introduce and explore a model for specialization at the front of a colony expanding synchronously into new territory. We show through numerical simulations that, by gaining fitness through accumulating mutations, progeny of the initial seed population can differentiate into distinct specialists. With competition and selection limited to the growth front, the emerging specialists first segregate into sectors, which then expand to dominate the entire population. We quantify the scaling of the fixation time with the size of the population and observe different behaviors corresponding to distinct universality classes: unbounded and bounded gains in fitness lead to superdiffusive (z=3/2) and diffusive (z=2) stochastic wanderings of the sector boundaries, respectively.
    Sprache Englisch
    Erscheinungsdatum 2023-09-25
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.108.L032402
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Scale-Dependent Heat Transport in Dissipative Media via Electromagnetic Fluctuations.

    Krüger, Matthias / Asheichyk, Kiryl / Kardar, Mehran / Golestanian, Ramin

    Physical review letters

    2024  Band 132, Heft 10, Seite(n) 106903

    Abstract: We develop a theory for heat transport via electromagnetic waves inside media, and use it to derive a spatially nonlocal thermal conductivity tensor, in terms of the electromagnetic Green's function and potential, for any given system. While typically ... ...

    Abstract We develop a theory for heat transport via electromagnetic waves inside media, and use it to derive a spatially nonlocal thermal conductivity tensor, in terms of the electromagnetic Green's function and potential, for any given system. While typically negligible for optically dense bulk media, the electromagnetic component of conductivity can be significant for optically dilute media, and shows regimes of Fourier transport as well as unhindered transport. Moreover, the electromagnetic contribution is relevant even for dense media, when in the presence of interfaces, as exemplified for the in-plane conductivity of a nanosheet, which shows a variety of phenomena, including absence of a Fourier regime.
    Sprache Englisch
    Erscheinungsdatum 2024-03-22
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.132.106903
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  3. Artikel ; Online: A Minimal Framework for Optimizing Vaccination Protocols Targeting Highly Mutable Pathogens.

    Mahdisoltani, Saeed / Murugan, Pranav / Chakraborty, Arup K / Kardar, Mehran

    ArXiv

    2024  

    Abstract: A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the Darwinian ... ...

    Abstract A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the Darwinian evolutionary process B cells undergo during immunization. The vaccination protocol dictates selection forces that steer affinity maturation to generate antibodies. We focus on determining the optimal selection forces exerted by a generic time-dependent vaccination protocol to maximize production of broadly neutralizing antibodies (bnAbs) that can protect against a broad spectrum of pathogen strains. The model lends itself to a path integral representation and operator approximations within a mean-field limit, providing guiding principles for optimizing time-dependent vaccine-induced selection forces to enhance bnAb generation. We compare our analytical mean-field results with the outcomes of stochastic simulations and discuss their similarities and differences.
    Sprache Englisch
    Erscheinungsdatum 2024-04-24
    Erscheinungsland United States
    Dokumenttyp Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Buch ; Online: Universal characterization of epitope immunodominance from a multi-scale model of clonal competition in germinal centers

    Ferretti, Federica / Kardar, Mehran

    2023  

    Abstract: We introduce a novel, multi-scale model for affinity maturation, which aims to capture the intra-clonal, inter-clonal and epitope-specific organization of the B cell population in a germinal center. We describe the evolution of the B cell population via ... ...

    Abstract We introduce a novel, multi-scale model for affinity maturation, which aims to capture the intra-clonal, inter-clonal and epitope-specific organization of the B cell population in a germinal center. We describe the evolution of the B cell population via a quasispecies dynamics, with species corresponding to unique B cell receptors (BCRs), where the desired multi-scale structure is reflected on the mutational connectivity of the accessible BCR space, and on the statistical properties of its fitness landscape. Within this mathematical framework, we study the competition among classes of BCRs targeting different antigen epitopes, and construct an effective \emph{immunogenic space} where epitope immunodominance relations can be universally characterized. We finally study how varying the relative composition of a mixture of antigens with variable and conserved domains allows for a parametric exploration of this space, and identify general principles for the rational design of two-antigen cocktails.

    Comment: 10 pages + 3 pages (appendix), 6 figures
    Schlagwörter Quantitative Biology - Populations and Evolution ; Condensed Matter - Statistical Mechanics ; Physics - Biological Physics
    Thema/Rubrik (Code) 612
    Erscheinungsdatum 2023-10-16
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

    Volltext online

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  5. Artikel ; Online: Active motion of passive asymmetric dumbbells in a non-equilibrium bath.

    Belan, Sergey / Kardar, Mehran

    The Journal of chemical physics

    2021  Band 154, Heft 2, Seite(n) 24109

    Abstract: Persistent motion of passive asymmetric bodies in non-equilibrium media has been experimentally observed in a variety of settings. However, fundamental constraints on the efficiency of such motion are not fully explored. Understanding such limits, and ... ...

    Abstract Persistent motion of passive asymmetric bodies in non-equilibrium media has been experimentally observed in a variety of settings. However, fundamental constraints on the efficiency of such motion are not fully explored. Understanding such limits, and ways to circumvent them, is important for efficient utilization of energy stored in agitated surroundings for purposes of taxis and transport. Here, we examine such issues in the context of erratic movements of a passive asymmetric dumbbell driven by non-equilibrium noise. For uncorrelated (white) noise, we find a (non-Boltzmann) joint probability distribution for the velocity and orientation, which indicates that the dumbbell preferentially moves along its symmetry axis. The dumbbell thus behaves as an Ornstein-Uhlenbeck walker, a prototype of active matter. Exploring the efficiency of this active motion, we show that in the over-damped limit, the persistence length l of the dumbbell is bound from above by half its mean size, while the propulsion speed v
    Sprache Englisch
    Erscheinungsdatum 2021-01-14
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0030623
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Z 4' 49/16: Hefte anzeigen

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  6. Artikel ; Online: How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease.

    Yin, Rose / Melton, Samuel / Huseby, Eric S / Kardar, Mehran / Chakraborty, Arup K

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

    2024  Band 121, Heft 11, Seite(n) e2318599121

    Abstract: T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. ... ...

    Abstract T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. These collective effects allow the T cell repertoire to respond to pathogens while suppressing autoimmunity due to circulating autoreactive T cells. Our computational studies show that increasing numbers of pathogenic peptides targeted by T cells during persistent or severe viral infections increase the probability of activating T cells that are weakly reactive to self-antigens (molecular mimicry). These T cells are easily re-activated by the self-antigens and contribute to exceeding the quorum threshold required to mount autoimmune responses. Rare peptides that activate many T cells are sampled more readily during severe/persistent infections than in acute infections, which amplifies these effects. Experiments in mice to test predictions from these mechanistic insights are suggested.
    Mesh-Begriff(e) Animals ; Mice ; Persistent Infection ; Peripheral Tolerance ; T-Lymphocytes ; Autoantigens ; Peptides ; Autoimmune Diseases
    Chemische Substanzen Autoantigens ; Peptides
    Sprache Englisch
    Erscheinungsdatum 2024-03-06
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2318599121
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1148: Hefte anzeigen Standort:
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  7. Buch ; Online: Specialization at an expanding front

    Li, Lauren H. / Kardar, Mehran

    2022  

    Abstract: As a population grows, spreading to new environments may favor specialization. In this paper, we introduce and explore a model for specialization at the front of a colony expanding synchronously into new territory. We show through numerical simulations ... ...

    Abstract As a population grows, spreading to new environments may favor specialization. In this paper, we introduce and explore a model for specialization at the front of a colony expanding synchronously into new territory. We show through numerical simulations that, by gaining fitness through accumulating mutations, progeny of the initial seed population can differentiate into distinct specialists. With competition and selection limited to the growth front, the emerging specialists first segregate into sectors, which then expand to dominate the entire population. We quantify the scaling of the fixation time with the size of the population and observe different behaviors corresponding to distinct universality classes: unbounded and bounded gains in fitness lead to superdiffusive ($z=3/2$) and diffusive ($z=2$) stochastic wanderings of the sector boundaries, respectively.

    Comment: 6+3 pages, 3+3 figures
    Schlagwörter Physics - Biological Physics ; Condensed Matter - Statistical Mechanics
    Thema/Rubrik (Code) 612
    Erscheinungsdatum 2022-10-11
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

    Volltext online

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  8. Artikel ; Online: Competition on the edge of an expanding population.

    Swartz, Daniel W / Lee, Hyunseok / Kardar, Mehran / Korolev, Kirill S

    ArXiv

    2023  

    Abstract: In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic ... ...

    Abstract In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (KPZ equation). We solved these equations and found three regimes, which are controlled solely by the expansion rates, solely by the competitive abilities, or by both. Collectively, our results provide a simple framework to study spatial competition.
    Sprache Englisch
    Erscheinungsdatum 2023-01-18
    Erscheinungsland United States
    Dokumenttyp Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: Polymer folding through active processes recreates features of genome organization.

    Goychuk, Andriy / Kannan, Deepti / Chakraborty, Arup K / Kardar, Mehran

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

    2023  Band 120, Heft 20, Seite(n) e2221726120

    Abstract: From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, ...

    Abstract From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate. Moreover, chromatin motion varies with genomic coordinate, pointing toward a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.
    Mesh-Begriff(e) Polymers/chemistry ; Chromatin/genetics ; Chromosomes/metabolism ; Genome ; Genomics
    Chemische Substanzen Polymers ; Chromatin
    Sprache Englisch
    Erscheinungsdatum 2023-05-08
    Erscheinungsland United States
    Dokumenttyp 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.2221726120
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 1148: Hefte anzeigen Standort:
    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. Artikel ; Online: Interplay between morphology and competition in two-dimensional colony expansion.

    Swartz, Daniel W / Lee, Hyunseok / Kardar, Mehran / Korolev, Kirill S

    Physical review. E

    2023  Band 108, Heft 3, Seite(n) L032301

    Abstract: In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic ... ...

    Abstract In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (Kardar-Parisi-Zhang equation). We solve these equations and find three regimes, which are controlled solely by the expansion rates, solely by the competitive abilities, or by both. Collectively, our results provide a simple framework to study spatial competition.
    Mesh-Begriff(e) Mutation ; Genetic Fitness ; Genetics, Population
    Sprache Englisch
    Erscheinungsdatum 2023-10-17
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.108.L032301
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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