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Anthuparambil ND, Timmermann S, Dargasz M, Retzbach S, Senft MD, Begam N, Ragulskaya A, Paulus M, Zhang F, Westermeier F, Sprung M, Schreiber F, Gutt C. Salt induced slowdown of kinetics and dynamics during thermal gelation of egg-yolk. J Chem Phys 2024; 161:055102. [PMID: 39105556 DOI: 10.1063/5.0219004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
We investigated the effect of the NaCl concentration (0.3-2M) on the structure and dynamics of hen egg yolk at room temperature and during thermal gelation at temperatures in the range of 66-90 °C utilizing low-dose x-ray photon correlation spectroscopy in ultra-small angle x-ray scattering geometry. With an increase in the salt concentration, we observe progressive structural and dynamic changes at room temperature, indicating the disruption of yolk components such as yolk-granules and yolk-plasma proteins. Temperature- and salt-dependent structural and dynamic investigations suggest a delay in the gel formation and aggregation of yolk low-density lipoproteins with increasing ionic strength. However, the time-temperature superposition relationship observed in all samples suggests an identical mechanism underlying protein aggregation-gelation with a temperature-dependent reaction rate. The sol-gel transition time extracted from kinetic and dynamic information follows Arrhenius's behavior, and the activation energy (460 kJ/mol) is found to be independent of the salt concentration.
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Affiliation(s)
| | | | | | - Sebastian Retzbach
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Maximilian D Senft
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | | | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | | | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, 57072 Siegen, Germany
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2
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Cho JH, Cerbino R, Bischofberger I. Emergence of Multiscale Dynamics in Colloidal Gels. PHYSICAL REVIEW LETTERS 2020; 124:088005. [PMID: 32167319 DOI: 10.1103/physrevlett.124.088005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
To gain insight into the kinetics of colloidal gel evolution at low particle volume fractions ϕ, we utilize differential dynamic microscopy to investigate particle aggregation, geometric percolation, and the subsequent transition to nonergodic dynamics. We report the emergence of unexpectedly rich multiscale dynamics upon the onset of nonergodicity, which separates the wave vectors q into three different regimes. In the high-q domain, the gel exhibits ϕ-independent internal vibrations of fractal clusters. The intermediate-q domain is dominated by density fluctuations at the length scale of the clusters, as evidenced by the q independence of the relaxation time τ. In the low-q domain, the scaling of τ as q^{-3} suggests that the network appears homogeneous. The transitions between these three regimes introduce two characteristic length scales, distinct from the cluster size.
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Affiliation(s)
- Jae Hyung Cho
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Roberto Cerbino
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via. F.lli Cervi 93, Segrate (MI) I-20090, Italy
| | - Irmgard Bischofberger
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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3
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Leitner DM, Pandey HD, Reid KM. Energy Transport across Interfaces in Biomolecular Systems. J Phys Chem B 2019; 123:9507-9524. [DOI: 10.1021/acs.jpcb.9b07086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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4
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Pal A, Eliazar I, Reuveni S. First Passage under Restart with Branching. PHYSICAL REVIEW LETTERS 2019; 122:020602. [PMID: 30720306 DOI: 10.1103/physrevlett.122.020602] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/02/2018] [Indexed: 05/27/2023]
Abstract
First passage under restart with branching is proposed as a generalization of first passage under restart. Strong motivation to study this generalization comes from the observation that restart with branching can expedite the completion of processes that cannot be expedited with simple restart; yet a sharp and quantitative formulation of this statement is still lacking. We develop a comprehensive theory of first passage under restart with branching. This reveals that two widely applied measures of statistical dispersion-the coefficient of variation and the Gini index-come together to determine how restart with branching affects the mean completion time of an arbitrary stochastic process. The universality of this result is demonstrated and its connection to extreme value theory is also pointed out and explored.
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Affiliation(s)
- Arnab Pal
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Shlomi Reuveni
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
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5
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Mahmoudi N, Stradner A. Structural arrest and dynamic localization in biocolloidal gels. SOFT MATTER 2017; 13:4629-4635. [PMID: 28613330 DOI: 10.1039/c7sm00496f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Casein micelles interacting via an entropic intermediate-ranged depletion attraction exhibit a fluid-to-gel transition due to arrested spinodal decomposition. The bicontinuous networked structure of the gel freezes shortly after formation. We determine the timescales of structural arrest from the build-up of network rigidity after pre-shear rejuvenation, and find that the arrest time as well as the plateau elastic modulus of the gel diverge as a function of the volume fraction and interaction potential. Moreover, we show using scaling from naïve mode coupling theory that their mechanical properties are dictated by their microscopic dynamics rather than their heterogeneous large scale structure.
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Affiliation(s)
- N Mahmoudi
- Adolphe Merkle Institute, University of Fribourg, Route de l'ancienne Papeterie 1, Marly, Switzerland. and Physical Chemistry, Lund University, Getingevägen 60, Lund, Sweden.
| | - A Stradner
- Physical Chemistry, Lund University, Getingevägen 60, Lund, Sweden.
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7
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Dolgushev M, Markelov DA, Fürstenberg F, Guérin T. Local orientational mobility in regular hyperbranched polymers. Phys Rev E 2016; 94:012502. [PMID: 27575171 DOI: 10.1103/physreve.94.012502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 11/07/2022]
Abstract
We study the dynamics of local bond orientation in regular hyperbranched polymers modeled by Vicsek fractals. The local dynamics is investigated through the temporal autocorrelation functions of single bonds and the corresponding relaxation forms of the complex dielectric susceptibility. We show that the dynamic behavior of single segments depends on their remoteness from the periphery rather than on the size of the whole macromolecule. Remarkably, the dynamics of the core segments (which are most remote from the periphery) shows a scaling behavior that differs from the dynamics obtained after structural average. We analyze the most relevant processes of single segment motion and provide an analytic approximation for the corresponding relaxation times. Furthermore, we describe an iterative method to calculate the orientational dynamics in the case of very large macromolecular sizes.
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Affiliation(s)
- Maxim Dolgushev
- Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany.,Institut Charles Sadron, Université de Strasbourg and CNRS, 23 rue du Loess, 67034 Strasbourg Cedex, France
| | - Denis A Markelov
- St. Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg, 199034, Russia.,St. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy pr. 49, St. Petersburg, 197101, Russia
| | - Florian Fürstenberg
- Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Thomas Guérin
- Laboratoire Ondes et Matière d'Aquitaine (LOMA), CNRS UMR 5798, Talence, France
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Reuveni S. Optimal Stochastic Restart Renders Fluctuations in First Passage Times Universal. PHYSICAL REVIEW LETTERS 2016; 116:170601. [PMID: 27176510 DOI: 10.1103/physrevlett.116.170601] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Indexed: 05/27/2023]
Abstract
Stochastic restart may drastically reduce the expected run time of a computer algorithm, expedite the completion of a complex search process, or increase the turnover rate of an enzymatic reaction. These diverse first-passage-time (FPT) processes seem to have very little in common but it is actually quite the other way around. Here we show that the relative standard deviation associated with the FPT of an optimally restarted process, i.e., one that is restarted at a constant (nonzero) rate which brings the mean FPT to a minimum, is always unity. We interpret, further generalize, and discuss this finding and the implications arising from it.
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Affiliation(s)
- Shlomi Reuveni
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
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9
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Liu H, Lin Y, Dolgushev M, Zhang Z. Dynamics of comb-of-comb networks. Phys Rev E 2016; 93:032502. [PMID: 27078400 DOI: 10.1103/physreve.93.032502] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 11/07/2022]
Abstract
The dynamics of complex networks, a current hot topic in many scientific fields, is often coded through the corresponding Laplacian matrix. The spectrum of this matrix carries the main features of the networks' dynamics. Here we consider the deterministic networks which can be viewed as "comb-of-comb" iterative structures. For their Laplacian spectra we find analytical equations involving Chebyshev polynomials whose properties allow one to analyze the spectra in deep. Here, in particular, we find that in the infinite size limit the corresponding spectral dimension goes as d(s) → 2. The d(s) leaves its fingerprint on many dynamical processes, as we exemplarily show by considering the dynamical properties of polymer networks, including single monomer displacement under a constant force, mechanical relaxation, and fluorescence depolarization.
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Affiliation(s)
- Hongxiao Liu
- School of Computer Science, Fudan University, Shanghai 200433, China.,Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Yuan Lin
- School of Computer Science, Fudan University, Shanghai 200433, China.,Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Maxim Dolgushev
- Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg, Germany.,Institut Charles Sadron, Université de Strasbourg and CNRS, 23 rue du Loess, 67034 Strasbourg Cedex, France
| | - Zhongzhi Zhang
- School of Computer Science, Fudan University, Shanghai 200433, China.,Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
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Rotbart T, Reuveni S, Urbakh M. Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:060101. [PMID: 26764608 DOI: 10.1103/physreve.92.060101] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Indexed: 05/27/2023]
Abstract
We study the effect of restart, and retry, on the mean completion time of a generic process. The need to do so arises in various branches of the sciences and we show that it can naturally be addressed by taking advantage of the classical reaction scheme of Michaelis and Menten. Stopping a process in its midst-only to start it all over again-may prolong, leave unchanged, or even shorten the time taken for its completion. Here we are interested in the optimal restart problem, i.e., in finding a restart rate which brings the mean completion time of a process to a minimum. We derive the governing equation for this problem and show that it is exactly solvable in cases of particular interest. We then continue to discover regimes at which solutions to the problem take on universal, details independent forms which further give rise to optimal scaling laws. The formalism we develop, and the results obtained, can be utilized when optimizing stochastic search processes and randomized computer algorithms. An immediate connection with kinetic proofreading is also noted and discussed.
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Affiliation(s)
- Tal Rotbart
- School of Chemistry, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Shlomi Reuveni
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Michael Urbakh
- School of Chemistry, Tel-Aviv University, Tel-Aviv 69978, Israel
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11
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Balankin AS. Effective degrees of freedom of a random walk on a fractal. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:062146. [PMID: 26764671 DOI: 10.1103/physreve.92.062146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Indexed: 06/05/2023]
Abstract
We argue that a non-Markovian random walk on a fractal can be treated as a Markovian process in a fractional dimensional space with a suitable metric. This allows us to define the fractional dimensional space allied to the fractal as the ν-dimensional space F(ν) equipped with the metric induced by the fractal topology. The relation between the number of effective spatial degrees of freedom of walkers on the fractal (ν) and fractal dimensionalities is deduced. The intrinsic time of random walk in F(ν) is inferred. The Laplacian operator in F(ν) is constructed. This allows us to map physical problems on fractals into the corresponding problems in F(ν). In this way, essential features of physics on fractals are revealed. Particularly, subdiffusion on path-connected fractals is elucidated. The Coulomb potential of a point charge on a fractal embedded in the Euclidean space is derived. Intriguing attributes of some types of fractals are highlighted.
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Affiliation(s)
- Alexander S Balankin
- Grupo "Mecánica Fractal," ESIME, Instituto Politécnico Nacional, México D.F., 07738, Mexico
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12
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Dolgushev M, Guérin T, Blumen A, Bénichou O, Voituriez R. Contact Kinetics in Fractal Macromolecules. PHYSICAL REVIEW LETTERS 2015; 115:208301. [PMID: 26613478 DOI: 10.1103/physrevlett.115.208301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Indexed: 06/05/2023]
Abstract
We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the mean first contact time for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the nonequilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the mean first contact time between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations.
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Affiliation(s)
- Maxim Dolgushev
- Physikalisches Institut, Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Thomas Guérin
- Université de Bordeaux and CNRS, Laboratoire Ondes et Matière d'Aquitaine (LOMA), UMR 5798, 33400 Talence, France
| | - Alexander Blumen
- Physikalisches Institut, Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Olivier Bénichou
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS/UPMC, 4 Place Jussieu, 75005 Paris, France
| | - Raphaël Voituriez
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS/UPMC, 4 Place Jussieu, 75005 Paris, France
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13
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Agbo JK, Gnanasekaran R, Leitner DM. Communication Maps: Exploring Energy Transport through Proteins and Water. Isr J Chem 2014. [DOI: 10.1002/ijch.201300139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Abstract
The Michaelis-Menten equation provides a hundred-year-old prediction by which any increase in the rate of substrate unbinding will decrease the rate of enzymatic turnover. Surprisingly, this prediction was never tested experimentally nor was it scrutinized using modern theoretical tools. Here we show that unbinding may also speed up enzymatic turnover--turning a spotlight to the fact that its actual role in enzymatic catalysis remains to be determined experimentally. Analytically constructing the unbinding phase space, we identify four distinct categories of unbinding: inhibitory, excitatory, superexcitatory, and restorative. A transition in which the effect of unbinding changes from inhibitory to excitatory as substrate concentrations increase, and an overlooked tradeoff between the speed and efficiency of enzymatic reactions, are naturally unveiled as a result. The theory presented herein motivates, and allows the interpretation of, groundbreaking experiments in which existing single-molecule manipulation techniques will be adapted for the purpose of measuring enzymatic turnover under a controlled variation of unbinding rates. As we hereby show, these experiments will not only shed first light on the role of unbinding but will also allow one to determine the time distribution required for the completion of the catalytic step in isolation from the rest of the enzymatic turnover cycle.
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15
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Fürstenberg F, Dolgushev M, Blumen A. Dynamics of semiflexible regular hyperbranched polymers. J Chem Phys 2013; 138:034904. [DOI: 10.1063/1.4775584] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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