@article{19701,
  abstract     = {Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.},
  author       = {Tkačik, Gašper and Wolde, Pieter Rein Ten},
  issn         = {1936-1238},
  journal      = {Annual Review of Biophysics},
  pages        = {249--274},
  publisher    = {Annual Reviews},
  title        = {{Information processing in biochemical networks}},
  doi          = {10.1146/annurev-biophys-060524-102720},
  volume       = {54},
  year         = {2025},
}

@article{18910,
  abstract     = {Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.},
  author       = {Schanda, Paul and Haran, Gilad},
  issn         = {1936-1238},
  journal      = {Annual Review of Biophysics},
  pages        = {247--273},
  publisher    = {Annual Reviews},
  title        = {{NMR and single-molecule FRET insights into fast protein motions and their relation to function}},
  doi          = {10.1146/annurev-biophys-070323-022428},
  volume       = {53},
  year         = {2024},
}

@article{17325,
  abstract     = {Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.},
  author       = {Lo, Wei Chang and Krasnopeeva, Ekaterina and Pilizota, Teuta},
  issn         = {1936-1238},
  journal      = {Annual Review of Biophysics},
  pages        = {487--510},
  publisher    = {Annual Reviews},
  title        = {{Bacterial Electrophysiology}},
  doi          = {10.1146/annurev-biophys-030822-032215},
  volume       = {53},
  year         = {2024},
}