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286 results on '"Betz, Timo"'

2. AdoptODE: Fusion of data and expert knowledge for modeling dynamical systems

Author

Lettermann, Leon, Jurado, Alejandro, Betz, Timo, Wörgötter, Florentin, and Herzog, Sebastian

Subjects
Physics - Data Analysis, Statistics and Probability, Nonlinear Sciences - Chaotic Dynamics, Physics - Biological Physics, Physics - Fluid Dynamics
Abstract

Building a representative model of a complex system remains a highly challenging problem. While by now there is basic understanding of most physical domains, model design is often hindered by lack of detail, for example concerning model dimensions or its relevant constraints. Here we present a novel model-building approach -- adoptODE -- augmenting basic system descriptions, based on expert knowledge in the form of ordinary differential equations, with continuous adjoint sensitivity analysis related to artificial neural network principles, based on observable data. With this we have created a general tool, that can be applied to any physical system described by ordinary differential equations. AdoptODE allows validating or extending the initial description, for example with different variables and constraints. This way one arrives at a better-optimised, representative low-dimensional model, which can fit existing data and predict novel experimental outcomes. We validate our method on five, quite different problem domains. (1) Kolmogorov model: Lotka Volterra model where we show the application of adoptODE to continuous-time Markov processes and the performance of adoptODE when working with noisy data. (2) Particle model: Interactive N-body, is a demonstration of the scalability of adoptODE and that even interactive system with a high number of elements can be reconstructed with high precision. (3) Excitable media (heart dynamics) by the Bueno\-Orovio\-Cherry\-Fenton model: AdoptODE can reconstruct the parameters of a high-dimensional model and fields for diffusion driven system for chaotic behaviour. (4) Fluid dynamics: Rayleigh-B\'enard Convection where a complete unknown field, the temperature, can be extracted from only velocity data. (5) New experimental data of Zebrafish embryogenesis: This is a case where we extend existing models with new variables.

Published
2023

4. Entropy bound for time reversal markers

Author

Knotz, Gabriel, Muenker, Till M., Betz, Timo, and Krüger, Matthias

Subjects
Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter
Abstract

We derive a bound for entropy production in terms of the mean of normalizable path-antisymmetric observables. The optimal observable for this bound is shown to be the signum of entropy production, which is often easier determined or estimated than entropy production itself. It can be preserved under coarse graining by use of a simple path grouping algorithm. We demonstrate this relation and its properties using a driven network on a ring, for which the bound saturates for short times for any driving strength. This work can open a way to systematic coarse graining of entropy production., Comment: 5 pages, 2 figures

Published
2023
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5. Roadmap for optical tweezers

Author

Volpe, Giovanni, Maragò, Onofrio M, Rubinsztein-Dunlop, Halina, Pesce, Giuseppe, Stilgoe, Alexander B, Volpe, Giorgio, Tkachenko, Georgiy, Truong, Viet Giang, Chormaic, Síle Nic, Kalantarifard, Fatemeh, Elahi, Parviz, Käll, Mikael, Callegari, Agnese, Marqués, Manuel I, Neves, Antonio AR, Moreira, Wendel L, Fontes, Adriana, Cesar, Carlos L, Saija, Rosalba, Saidi, Abir, Beck, Paul, Eismann, Jörg S, Banzer, Peter, Fernandes, Thales FD, Pedaci, Francesco, Bowen, Warwick P, Vaippully, Rahul, Lokesh, Muruga, Roy, Basudev, Thalhammer-Thurner, Gregor, Ritsch-Marte, Monika, García, Laura Pérez, Arzola, Alejandro V, Castillo, Isaac Pérez, Argun, Aykut, Muenker, Till M, Vos, Bart E, Betz, Timo, Cristiani, Ilaria, Minzioni, Paolo, Reece, Peter J, Wang, Fan, McGloin, David, Ndukaife, Justus C, Quidant, Romain, Roberts, Reece P, Laplane, Cyril, Volz, Thomas, Gordon, Reuven, Hanstorp, Dag, Marmolejo, Javier Tello, Bruce, Graham D, Dholakia, Kishan, Li, Tongcang, Brzobohatý, Oto, Simpson, Stephen H, Zemánek, Pavel, Ritort, Felix, Roichman, Yael, Bobkova, Valeriia, Wittkowski, Raphael, Denz, Cornelia, Kumar, GV Pavan, Foti, Antonino, Donato, Maria Grazia, Gucciardi, Pietro G, Gardini, Lucia, Bianchi, Giulio, Kashchuk, Anatolii V, Capitanio, Marco, Paterson, Lynn, Jones, Philip H, Berg-Sørensen, Kirstine, Barooji, Younes F, Oddershede, Lene B, Pouladian, Pegah, Preece, Daryl, Adiels, Caroline Beck, De Luca, Anna Chiara, Magazzù, Alessandro, Ciriza, David Bronte, Iatì, Maria Antonia, and Swartzlander, Grover A

Subjects
Physical Sciences, Classical Physics, Nanotechnology, Bioengineering, optical tweezers, optical trapping, optical manipulation, Atomic, molecular and optical physics, Quantum physics
Abstract

Optical tweezers are tools made of light that enable contactless pushing, trapping, and manipulation of objects, ranging from atoms to space light sails. Since the pioneering work by Arthur Ashkin in the 1970s, optical tweezers have evolved into sophisticated instruments and have been employed in a broad range of applications in the life sciences, physics, and engineering. These include accurate force and torque measurement at the femtonewton level, microrheology of complex fluids, single micro- and nano-particle spectroscopy, single-cell analysis, and statistical-physics experiments. This roadmap provides insights into current investigations involving optical forces and optical tweezers from their theoretical foundations to designs and setups. It also offers perspectives for applications to a wide range of research fields, from biophysics to space exploration.

Published
2023

6. Roadmap for Optical Tweezers

Author

Volpe, Giovanni, Maragò, Onofrio M., Rubinzstein-Dunlop, Halina, Pesce, Giuseppe, Stilgoe, Alexander B., Volpe, Giorgio, Tkachenko, Georgiy, Truong, Viet Giang, Chormaic, Síle Nic, Kalantarifard, Fatemeh, Elahi, Parviz, Käll, Mikael, Callegari, Agnese, Marqués, Manuel I., Neves, Antonio A. R., Moreira, Wendel L., Fontes, Adriana, Cesar, Carlos L., Saija, Rosalba, Saidi, Abir, Beck, Paul, Eismann, Jörg S., Banzer, Peter, Fernandes, Thales F. D., Pedaci, Francesco, Bowen, Warwick P, Vaippully, Rahul, Lokesh, Muruga, Roy, Basudev, Thalhammer, Gregor, Ritsch-Marte, Monika, García, Laura Pérez, Arzola, Alejandro V., Castillo, Isaac Pérez, Argun, Aykut, Muenker, Till M., Vos, Bart E., Betz, Timo, Cristiani, Ilaria, Minzioni, Paolo, Reece, Peter J., Wang, Fan, McGloin, David, Ndukaife, Justus C., Quidant, Romain, Roberts, Reece P., Laplane, Cyril, Volz, Thomas, Gordon, Reuven, Hanstorp, Dag, Marmolejo, Javier Tello, Bruce, Graham D., Dholakia, Kishan, Li, Tongcang, Brzobohatý, Oto, Simpson, Stephen H., Zemánek, Pavel, Ritort, Felix, Roichman, Yael, Bobkova, Valeriia, Wittkowski, Raphael, Denz, Cornelia, Kumar, G. V. Pavan, Foti, Antonino, Donato, Maria Grazia, Gucciardi, Pietro G., Gardini, L., Bianchi, G., Kashchuk, A., Capitanio, M., Paterson, Lynn, Jones, P. H., Berg-Sørensen, Kirstine, Barooji, Younes F., Oddershede, Lene B., Pouladian, Pegah, Preece, Daryl, Adiels, Caroline Beck, De Luca, Anna Chiara, Magazzù, A., Ciriza, D. Bronte, Iatì, M. A., and Swartzlander, Grover A.

Subjects
Physics - Optics, Condensed Matter - Soft Condensed Matter
Abstract

Optical tweezers are tools made of light that enable contactless pushing, trapping, and manipulation of objects ranging from atoms to space light sails. Since the pioneering work by Arthur Ashkin in the 1970s, optical tweezers have evolved into sophisticated instruments and have been employed in a broad range of applications in life sciences, physics, and engineering. These include accurate force and torque measurement at the femtonewton level, microrheology of complex fluids, single micro- and nanoparticle spectroscopy, single-cell analysis, and statistical-physics experiments. This roadmap provides insights into current investigations involving optical forces and optical tweezers from their theoretical foundations to designs and setups. It also offers perspectives for applications to a wide range of research fields, from biophysics to space exploration., Comment: 181 pages, 61 figures

Published
2022

10. Fluctuations of a membrane nanotube covered with an actin sleeve

Author

Allard, Antoine, Valentino, Fabrice, Sykes, Cécile, Betz, Timo, and Campillo, Clément

Subjects
Physics - Biological Physics
Abstract

Many biological functions rely on the reshaping of cell membranes, in particular into nanotubes, which are covered in vivo by dynamic actin networks. Nanotubes are subject to thermal fluctuations, but the effect of these on cell functions is unknown. Here, we form nanotubes from liposomes using an optically trapped bead adhering to the liposome membrane. From the power spectral density of this bead, we study the nanotube fluctuations in the range of membrane tensions measured in vivo. We show that an actin sleeve covering the nanotube damps its high frequency fluctuations because of the network viscoelasticity. Our work paves the way for further studies on the effect of nanotube fluctuations in cellular functions.

Published
2020
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12. Fluctuations in active membranes

Author

Turlier, Hervé and Betz, Timo

Subjects
Physics - Biological Physics, 92C05
Abstract

Active contributions to fluctuations are a direct consequence of metabolic energy consumption in living cells. Such metabolic processes continuously create active forces, which deform the membrane to control motility, proliferation as well as homeostasis. Membrane fluctuations contain therefore valuable information on the nature of active forces, but classical analysis of membrane fluctuations has been primarily centered on purely thermal driving. This chapter provides an overview of relevant experimental and theoretical approaches to measure, analyze and model active membrane fluctuations. In the focus of the discussion remains the intrinsic problem that the sole fluctuation analysis may not be sufficient to separate active from thermal contributions, since the presence of activity may modify membrane mechanical properties themselves. By combining independent measurements of spontaneous fluctuations and mechanical response, it is possible to directly quantify time and energy-scales of the active contributions, allowing for a refinement of current theoretical descriptions of active membranes., Comment: 38 pages, 9 figures, book chapter

Published
2017

16. Nonequilibrium dissipation in living oocytes

Author

Fodor, Étienne, Ahmed, Wylie W., Almonacid, Maria, Bussonnier, Matthias, Gov, Nir S., Verlhac, Marie-Hélène, Betz, Timo, Visco, Paolo, and van Wijland, Frédéric

Subjects
Quantitative Biology - Subcellular Processes, Condensed Matter - Soft Condensed Matter, Condensed Matter - Statistical Mechanics, Physics - Biological Physics
Abstract

Living organisms are inherently out-of-equilibrium systems. We employ new developments in stochastic energetics and rely on a minimal microscopic model to predict the amount of mechanical energy dissipated by such dynamics. Our model includes complex rheological effects and nonequilibrium stochastic forces. By performing active microrheology and tracking micron-sized vesicles in the cytoplasm of living oocytes, we provide unprecedented measurements of the spectrum of dissipated energy. We show that our model is fully consistent with the experimental data, and we use it to offer predictions for the injection and dissipation energy scales involved in active fluctuations., Comment: 5 pages, 2 figures

Published
2015
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17. Active mechanics reveal molecular-scale force kinetics in living oocytes

Author

Ahmed, Wylie W., Fodor, Etienne, Almonacid, Maria, Bussonnier, Matthias, Verlhac, Marie-Helene, Gov, Nir S., Visco, Paolo, van Wijland, Frederic, and Betz, Timo

Subjects
Physics - Biological Physics, Condensed Matter - Soft Condensed Matter, Quantitative Biology - Quantitative Methods, Quantitative Biology - Subcellular Processes
Abstract

Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and facilitate enhanced motion. The kinetics of molecular motors have been precisely characterized in-vitro by single molecule approaches, however, their in-vivo behavior remains elusive. Here, we study the active diffusion of vesicles in mouse oocytes, where this process plays a key role in nuclear positioning during development, and combine an experimental and theoretical framework to extract molecular-scale force kinetics (force, power-stroke, and velocity) of the in-vivo active process. Assuming a single dominant process, we find that the nonequilibrium activity induces rapid kicks of duration $\tau \sim$ 300 $\mu$s resulting in an average force of $F \sim$ 0.4 pN on vesicles in in-vivo oocytes, remarkably similar to the kinetics of in-vitro myosin-V. Our results reveal that measuring in-vivo active fluctuations allows extraction of the molecular-scale activity in agreement with single-molecule studies and demonstrates a mesoscopic framework to access force kinetics., Comment: 20 pages, 4 figures, see ancillary files for Supplementary Materials, * equally contributing authors

Published
2015
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20. Roadmap for optical tweezers

Author

NASA Innovative Advanced Concepts, Australian Research Council, Japan Society for the Promotion of Science, Boğaziçi Üniversity, Novo Nordisk UK Research Foundation, Knut and Alice Wallenberg Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Universidad Autónoma de Madrid, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Universidade Federal do Ceará, Agenzia Spaziale Italiana, Istituto Nazionale di Astrofisica, Agence Nationale de la Recherche (France), Wellcome Trust, Austrian Science Fund, Universidad Nacional Autónoma de México, European Commission, European Research Council, German Research Foundation, Natural Sciences and Engineering Research Council of Canada, Swedish Research Council, Engineering and Physical Sciences Research Council (UK), Office of Naval Research (US), National Science Foundation (US), Institute of Geology of the Czech Academy of Sciences, Czech Science Foundation, Generalitat de Catalunya, University of Münster, Department of Science and Technology (India), Human Frontier Science Program, Biotechnology and Biological Sciences Research Council (UK), Medical Research Council (UK), Danish National Research Foundation, Independent Research Fund Denmark, Beckman Institute, Associazione Italiana per la Ricerca sul Cancro, Volpe, Giovanni [0000-0001-5057-1846], Maragò, Onofrio M. [0000-0002-7220-8527], Rubinsztein-Dunlop, Halina [0000-0002-8332-2309], Stilgoe, Alexander B. [0000-0002-9299-5695], Volpe, Giorgio [0000-0001-9993-5348], Truong, Viet Giang [0000-0003-3589-7850], Chormaic, Síle Nic [0000-0003-4276-2014], Elahi, Parviz [0000-0003-3545-8436], Käll, Mikael [0000-0002-1163-0345], Callegari, Agnese [0000-0002-4488-4106], Neves, Antonio A. R. [0000-0002-2615-8573], Eismann, Jörg S. [0000-0002-2495-4613], Banzer, Peter [0000-0002-6336-6953], Roy, Basudev [0000-0003-0737-2889], Thalhammer-Thurner, Gregor [0000-0002-3948-8045], Ritsch-Marte, Monika [0000-0002-5945-546X], Pérez Castillo, Isaac0000-0001-7622-9440, Muenker, Till M. [0000-0003-3225-8746], Vos, Bart E. [0000-0002-4325-6298], Betz, Timo [0000-0002-1548-0655], Reece, Peter J. [0000-0003-4852-3735], McGloin, David [0000-0002-0075-4481], Gordon, Reuven [0000-0002-1485-6067], Bruce, Graham D. [0000-0003-3403-0614], Dholakia, Kishan [0000-0001-6534-9009], Roichman, Yael [0000-0003-1927-4506], Bobkova, Valeriia [0000-0003-4080-9069], Wittkowski, Raphael [0000-0003-4881-9173], Denz, Cornelia [0000-0002-7292-2499], Pavan Kumar, G. V. [0000-0002-4036-7187], Foti, Antonino [0000-0002-9824-3099], Donato, Maria Grazia [0000-0002-7580-3137], Gucciardi, Pietro G. [0000-0003-1826-9174], Gardini, Lucia [0000-0003-0923-9221], Kashchuk, Anatolii V. [0000-0002-2364-9393], Capitanio, Marco [0000-0002-9799-9353], Paterson, Lynn [0000-0003-0493-5041], Jones, Philip H. [0000-0002-0860-631X], Berg-Sørensen, Kirstine [0000-0002-9977-3980], Oddershede, Lene B. [0000-0003-2923-2844], Magazzù, Alessandro [0000-0003-1247-2702], Bronte Ciriza, David [0000-0002-5874-6601], Iatì, Maria Antonia [0000-0002-3576-8656], Swartzlander, Grover A. [0000-0003-3513-2225], Volpe, Giovanni, Maragò, Onofrio M., Rubinsztein-Dunlop, Halina, Pesce, Giuseppe, Stilgoe, Alexander B., Volpe, Giorgio, Tkachenko, Georgiy, Truong, Viet Giang, Chormaic, Síle Nic, Kalantarifard, Fatemeh, Elahi, Parviz, Käll, Mikael, Callegari, Agnese, Marqués, Manuel I., Neves, Antonio A. R., Moreira, Wendel L., Fontes, Adriana, César, Carlos L., Saija, Rosalba, Saidi, Abir, Beck, Paul, Eismann, Jörg S., Banzer, Peter, Fernandes, Thales F. D., Pedaci, Francesco, Bowen, Warwick P., Vaippully, Rahul, Lokesh, Muruga, Roy, Basudev, Thalhammer-Thurner, Gregor, Ritsch-Marte, Monika, Pérez García, Laura, Arzola, Alejandro V., Pérez Castillo, Isaac, Argun, Aykut, Muenker, Till M., Vos, Bart E., Betz, Timo, Cristiani, Ilaria, Minzioni, Paolo, Reece, Peter J., Wang, Fan, McGloin, David, Ndukaife, Justus C., Quidant, Romain, Roberts, Reece P., Laplane, Cyril, Volz, Thomas, Gordon, Reuven, Hanstorp, Dag, Tello Marmolejo, Javier, Bruce, Graham D., Dholakia, Kishan, Li, Tongcang, Brzobohatý, Oto, Simpson, Stephen H., Zemánek, Pavel, Ritort, Félix, Roichman, Yael, Bobkova, Valeriia, Wittkowski, Raphael, Denz, Cornelia, Pavan Kumar, G. V., Foti, Antonino, Donato, Maria Grazia, Gucciardi, Pietro G., Gardini, Lucia, Bianchi, Giulio, Kashchuk, Anatolii V., Capitanio, Marco, Paterson, Lynn, Jones, Philip H., Berg-Sørensen, Kirstine, Barooji, Younes F., Oddershede, Lene B., Pouladian, Pegah, Preece, Daryl, Adiels, Caroline Beck, De Luca, Anna Chiara, Magazzù, Alessandro, Bronte Ciriza, David, Iatì, Maria Antonia, Swartzlander, Grover A., NASA Innovative Advanced Concepts, Australian Research Council, Japan Society for the Promotion of Science, Boğaziçi Üniversity, Novo Nordisk UK Research Foundation, Knut and Alice Wallenberg Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Universidad Autónoma de Madrid, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Universidade Federal do Ceará, Agenzia Spaziale Italiana, Istituto Nazionale di Astrofisica, Agence Nationale de la Recherche (France), Wellcome Trust, Austrian Science Fund, Universidad Nacional Autónoma de México, European Commission, European Research Council, German Research Foundation, Natural Sciences and Engineering Research Council of Canada, Swedish Research Council, Engineering and Physical Sciences Research Council (UK), Office of Naval Research (US), National Science Foundation (US), Institute of Geology of the Czech Academy of Sciences, Czech Science Foundation, Generalitat de Catalunya, University of Münster, Department of Science and Technology (India), Human Frontier Science Program, Biotechnology and Biological Sciences Research Council (UK), Medical Research Council (UK), Danish National Research Foundation, Independent Research Fund Denmark, Beckman Institute, Associazione Italiana per la Ricerca sul Cancro, Volpe, Giovanni [0000-0001-5057-1846], Maragò, Onofrio M. [0000-0002-7220-8527], Rubinsztein-Dunlop, Halina [0000-0002-8332-2309], Stilgoe, Alexander B. [0000-0002-9299-5695], Volpe, Giorgio [0000-0001-9993-5348], Truong, Viet Giang [0000-0003-3589-7850], Chormaic, Síle Nic [0000-0003-4276-2014], Elahi, Parviz [0000-0003-3545-8436], Käll, Mikael [0000-0002-1163-0345], Callegari, Agnese [0000-0002-4488-4106], Neves, Antonio A. R. [0000-0002-2615-8573], Eismann, Jörg S. [0000-0002-2495-4613], Banzer, Peter [0000-0002-6336-6953], Roy, Basudev [0000-0003-0737-2889], Thalhammer-Thurner, Gregor [0000-0002-3948-8045], Ritsch-Marte, Monika [0000-0002-5945-546X], Pérez Castillo, Isaac0000-0001-7622-9440, Muenker, Till M. [0000-0003-3225-8746], Vos, Bart E. [0000-0002-4325-6298], Betz, Timo [0000-0002-1548-0655], Reece, Peter J. [0000-0003-4852-3735], McGloin, David [0000-0002-0075-4481], Gordon, Reuven [0000-0002-1485-6067], Bruce, Graham D. [0000-0003-3403-0614], Dholakia, Kishan [0000-0001-6534-9009], Roichman, Yael [0000-0003-1927-4506], Bobkova, Valeriia [0000-0003-4080-9069], Wittkowski, Raphael [0000-0003-4881-9173], Denz, Cornelia [0000-0002-7292-2499], Pavan Kumar, G. V. [0000-0002-4036-7187], Foti, Antonino [0000-0002-9824-3099], Donato, Maria Grazia [0000-0002-7580-3137], Gucciardi, Pietro G. [0000-0003-1826-9174], Gardini, Lucia [0000-0003-0923-9221], Kashchuk, Anatolii V. [0000-0002-2364-9393], Capitanio, Marco [0000-0002-9799-9353], Paterson, Lynn [0000-0003-0493-5041], Jones, Philip H. [0000-0002-0860-631X], Berg-Sørensen, Kirstine [0000-0002-9977-3980], Oddershede, Lene B. [0000-0003-2923-2844], Magazzù, Alessandro [0000-0003-1247-2702], Bronte Ciriza, David [0000-0002-5874-6601], Iatì, Maria Antonia [0000-0002-3576-8656], Swartzlander, Grover A. [0000-0003-3513-2225], Volpe, Giovanni, Maragò, Onofrio M., Rubinsztein-Dunlop, Halina, Pesce, Giuseppe, Stilgoe, Alexander B., Volpe, Giorgio, Tkachenko, Georgiy, Truong, Viet Giang, Chormaic, Síle Nic, Kalantarifard, Fatemeh, Elahi, Parviz, Käll, Mikael, Callegari, Agnese, Marqués, Manuel I., Neves, Antonio A. R., Moreira, Wendel L., Fontes, Adriana, César, Carlos L., Saija, Rosalba, Saidi, Abir, Beck, Paul, Eismann, Jörg S., Banzer, Peter, Fernandes, Thales F. D., Pedaci, Francesco, Bowen, Warwick P., Vaippully, Rahul, Lokesh, Muruga, Roy, Basudev, Thalhammer-Thurner, Gregor, Ritsch-Marte, Monika, Pérez García, Laura, Arzola, Alejandro V., Pérez Castillo, Isaac, Argun, Aykut, Muenker, Till M., Vos, Bart E., Betz, Timo, Cristiani, Ilaria, Minzioni, Paolo, Reece, Peter J., Wang, Fan, McGloin, David, Ndukaife, Justus C., Quidant, Romain, Roberts, Reece P., Laplane, Cyril, Volz, Thomas, Gordon, Reuven, Hanstorp, Dag, Tello Marmolejo, Javier, Bruce, Graham D., Dholakia, Kishan, Li, Tongcang, Brzobohatý, Oto, Simpson, Stephen H., Zemánek, Pavel, Ritort, Félix, Roichman, Yael, Bobkova, Valeriia, Wittkowski, Raphael, Denz, Cornelia, Pavan Kumar, G. V., Foti, Antonino, Donato, Maria Grazia, Gucciardi, Pietro G., Gardini, Lucia, Bianchi, Giulio, Kashchuk, Anatolii V., Capitanio, Marco, Paterson, Lynn, Jones, Philip H., Berg-Sørensen, Kirstine, Barooji, Younes F., Oddershede, Lene B., Pouladian, Pegah, Preece, Daryl, Adiels, Caroline Beck, De Luca, Anna Chiara, Magazzù, Alessandro, Bronte Ciriza, David, Iatì, Maria Antonia, and Swartzlander, Grover A.

Abstract

Optical tweezers are tools made of light that enable contactless pushing, trapping, and manipulation of objects, ranging from atoms to space light sails. Since the pioneering work by Arthur Ashkin in the 1970s, optical tweezers have evolved into sophisticated instruments and have been employed in a broad range of applications in the life sciences, physics, and engineering. These include accurate force and torque measurement at the femtonewton level, microrheology of complex fluids, single micro- and nano-particle spectroscopy, single-cell analysis, and statistical-physics experiments. This roadmap provides insights into current investigations involving optical forces and optical tweezers from their theoretical foundations to designs and setups. It also offers perspectives for applications to a wide range of research fields, from biophysics to space exploration.

Published
2023

22. List of Contributors

Author

Akinyi, Teckla, primary, Balland, Martial, additional, Barriga, Elias H., additional, Betz, Timo, additional, Bhatt, Manish, additional, Borja, Cristian, additional, Boudou, Thomas, additional, Brochard-Wyart, Françoise, additional, Cappello, Giovanni, additional, Catheline, Stefan, additional, Clark, Andrew G., additional, Cloutier, Guy, additional, Espina, Jaime A., additional, Gonzalez-Rodriguez, David, additional, Grasland-Mongrain, Pol, additional, Guevorkian, Karine, additional, Milivojevic, Milan, additional, Moral, Elena, additional, Muñoz, Jose J., additional, Pajic-Lijakovic, Ivana, additional, Petrolli, Vanni, additional, and Saraiva, Joana E., additional

Published
2021
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24. Culture substrate stiffness impacts human myoblast contractility-dependent proliferation and nuclear envelope wrinkling.

Author

Jo Nguyen, Lu Wang, Wen Lei, Yechen Hu, Gulati, Nitya, Chavez-Madero, Carolina, Ahn, Henry, Ginsberg, Howard J., Krawetz, Roman, Brandt, Matthias, Betz, Timo, and Gilbert, Penney M.

Subjects
NUCLEAR nonproliferation, MYOBLASTS, EXTRACELLULAR matrix, CELL metabolism, STEM cells, MUSCLE cells, CELL culture, NUCLEAR membranes
Abstract

Understanding how biophysical and biochemical microenvironmental cues together influence the regenerative activities of muscle stem cells and their progeny is crucial in strategizing remedies for pathological dysregulation of these cues in aging and disease. In this study, we investigated the cell-level influences of extracellular matrix (ECM) ligands and culture substrate stiffness on primary human myoblast contractility and proliferation within 16 h of plating and found that tethered fibronectin led to stronger stiffness-dependent responses compared to laminin and collagen. A proteome-wide analysis further uncovered cell metabolism, cytoskeletal and nuclear component regulation distinctions between cells cultured on soft and stiff substrates. Interestingly, we found that softer substrates increased the incidence of myoblasts with a wrinkled nucleus, and that the extent of wrinkling could predict Ki67 (also known as MKI67) expression. Nuclear wrinkling and Ki67 expression could be controlled by pharmacological manipulation of cellular contractility, offering a potential cellular mechanism. These results provide new insights into the regulation of human myoblast stiffness-dependent contractility response by ECM ligands and highlight a link between myoblast contractility and proliferation. [ABSTRACT FROM AUTHOR]

Published
2024
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28. Culture substrate stiffness impacts human myoblast contractility-dependent proliferation and nuclear envelope wrinkling

Author

Nguyen, Jo, primary, Wang, Lu, additional, Lei, Wen, additional, Hu, Yechen, additional, Gulati, Nitya, additional, Chavez-Madero, Carolina, additional, Ahn, Henry, additional, Ginsberg, Howard J., additional, Krawetz, Roman, additional, Brandt, Matthias, additional, Betz, Timo, additional, and Gilbert, Penney M., additional

Published
2023
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32. Dystrophin is a mechanical tension modulator

Author

Hofemeier, Arne D., primary, Muenker, Till M., additional, Herkenrath, Fabian, additional, Ristau, Mariam, additional, Brandt, Matthias, additional, Shahriyari, Mina, additional, Tiburcy, Malte, additional, Zimmermann, Wolfram H., additional, Lenz, Christof, additional, Mamchaoui, Kamel, additional, Bigot, Anne, additional, Gilbert, Penney M., additional, and Betz, Timo, additional

Published
2022
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33. PhysNODE: Fusion of data and expert knowledge for modeling dynamical systems

Author

Lettermann, Leon, Jurado, Alejandro, Betz, Timo, Wörgötter, Florentin, and Herzog, Sebastian

Subjects
Biological Physics (physics.bio-ph), Physics - Data Analysis, Statistics and Probability, Fluid Dynamics (physics.flu-dyn), FOS: Physical sciences, Physics - Biological Physics, Physics - Fluid Dynamics, Chaotic Dynamics (nlin.CD), Nonlinear Sciences - Chaotic Dynamics, Data Analysis, Statistics and Probability (physics.data-an)
Abstract

Building a representative model of a complex system remains a highly challenging problem. While by now there is basic understanding of most physical domains, model design is often hindered by lack of detail, for example concerning model dimensions or its relevant constraints. Here we present a novel model-building approach -- physNODE -- augmenting basic system descriptions, based on expert knowledge in the form of ordinary differential equations, with continuous adjoint sensitivity analysis related to artificial neural network principles, based on observable data. With this we have created a general tool, that can be applied to any physical system described by ordinary differential equations. PhysNODE allows validating or extending the initial description, for example with different variables and constraints. This way one arrives at a better-optimised, representative low-dimensional model, which can fit existing data and predict novel experimental outcomes. We validate our method on five, quite different problem domains. (1) Kolmogorov model: Lotka Volterra model where we show the application of physNODE to continuous-time Markov processes and the performance of physNODE when working with noisy data. (2) Particle model: Interactive N-body, is a demonstration of the scalability of physNODE and that even interactive system with a high number of elements can be reconstructed with high precision. (3) Excitable media (heart dynamics) by the Bueno\-Orovio\-Cherry\-Fenton model: PhysNODE can reconstruct the parameters of a high-dimensional model and fields for diffusion driven system for chaotic behaviour. (4) Fluid dynamics: Rayleigh-B\'enard Convection where a complete unknown field, the temperature, can be extracted from only velocity data. (5) New experimental data of Zebrafish embryogenesis: This is a case where we extend existing models with new variables.

Published
2023
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35. Alarming and Calming: Opposing Roles of S100A8/S100A9 Dimers and Tetramers on Monocytes

Author

Russo, Antonella, primary, Schürmann, Hendrik, additional, Brandt, Matthias, additional, Scholz, Katja, additional, Matos, Anna Livia L., additional, Grill, David, additional, Revenstorff, Julian, additional, Rembrink, Maximilian, additional, von Wulffen, Meike, additional, Fischer‐Riepe, Lena, additional, Hanley, Peter J., additional, Häcker, Hans, additional, Prünster, Monika, additional, Sánchez‐Madrid, Francisco, additional, Hermann, Sven, additional, Klotz, Luisa, additional, Gerke, Volker, additional, Betz, Timo, additional, Vogl, Thomas, additional, and Roth, Johannes, additional

Published
2022
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44. A JAM-A–tetraspanin–αvβ5 integrin complex regulates contact inhibition of locomotion

Author

Kummer, Daniel, primary, Steinbacher, Tim, additional, Thölmann, Sonja, additional, Schwietzer, Mariel Flavia, additional, Hartmann, Christian, additional, Horenkamp, Simone, additional, Demuth, Sabrina, additional, Peddibhotla, Swetha S.D., additional, Brinkmann, Frauke, additional, Kemper, Björn, additional, Schnekenburger, Jürgen, additional, Brandt, Matthias, additional, Betz, Timo, additional, Liashkovich, Ivan, additional, Kouzel, Ivan U., additional, Shahin, Victor, additional, Corvaia, Nathalie, additional, Rottner, Klemens, additional, Tarbashevich, Katsiaryna, additional, Raz, Erez, additional, Greune, Lilo, additional, Schmidt, M. Alexander, additional, Gerke, Volker, additional, and Ebnet, Klaus, additional

Published
2022
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46. Pressure Drives Rapid Burst‐Like Coordinated Cellular Motion from 3D Cancer Aggregates (Adv. Sci. 6/2022)

Author

Raghuraman, Swetha, primary, Schubert, Ann‐Sophie, additional, Bröker, Stephan, additional, Jurado, Alejandro, additional, Müller, Annika, additional, Brandt, Matthias, additional, Vos, Bart E., additional, Hofemeier, Arne D., additional, Abbasi, Fatemeh, additional, Stehling, Martin, additional, Wittkowski, Raphael, additional, Ivaska, Johanna, additional, and Betz, Timo, additional

Published
2022
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