Photosynthesis is arguably the fundamental process of Life, since it enables energy from the Sun to enter the food-chain on Earth. It is a remarkable non-equilibrium process in which photons are converted to many-body excitations which traverse a complex biomolecular membrane, getting captured and fueling chemical reactions within a reaction-center in order to produce nutrients. The precise nature of these dynamical processes -- which lie at the interface between quantum and classical behaviour, and involve both noise and coordination -- are still being explored. Here we focus on a striking recent empirical finding concerning an illumination-driven transition in the biomolecular membrane architecture of {\it Rsp. Photometricum} purple bacteria. Using stochastic realisations to describe a hopping rate model for excitation transfer, we show numerically and analytically that this surprising shift in preferred architectures can be traced to the interplay between the excitation kinetics and the reaction center dynamics. The net effect is that the bacteria profit from efficient metabolism at low illumination intensities while using dissipation to avoid an oversupply of energy at high illumination intensities.
Light-harvesting complexes in natural photosynthetic systems, such as those in purple bacteria, consist of photo-reactive chromophores embedded in densely packed "antenna" systems organized in well-defined nanostructures. In the case of purple bacteria, the chromophore antennas are composed of natural J-aggregates such as bacteriochlorophylls and carotenoids. Inspired by the molecular composition of such biological systems, we create a library of organic materials composed of densely packed J-aggregates in a polymeric matrix, in which the matrix mimics a protein scaffold. This library of organ…
The study of how photosynthetic organisms convert light offers insight not only into nature's evolutionary process, but may also give clues as to how best to design and manipulate artificial photosynthetic systems -- and also how far we can drive natural photosynthetic systems beyond normal operating conditions, so that they can harvest energy for us under otherwise extreme conditions. In addition to its interest from a basic scientific perspective, therefore, the goal to develop a deep quantitative understanding of photosynthesis offers the potential payoff of enhancing our current arsenal of…
Light-harvesting bacteria Rhodospirillum Photometricum were recently found to adopt strikingly different architectures depending on illumination conditions. We present analytic and numerical calculations which explain this observation by quantifying a dynamical interplay between excitation transfer kinetics and reaction center cycling. High light-intensity membranes (HLIM) exploit dissipation as a photo-protective mechanism, thereby safeguarding a steady supply of chemical energy, while low light-intensity membranes (LLIM) efficiently process unused illumination intensity by channelling it to …
Motivated by observations of the dynamics of {\it Myxococcus xanthus}, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but release a chemical chemoattractant at a steady state. The bacteria senses the chemical that it produces. The probability of direction reversals is modeled as a function of both the absolute level of chemoattractant sensed directly under each cell as well as the gradient sensed across the length of the cell. If the chemical does not degrade or diffuse rapidly,…
Bacterial colonies are abundant on living and nonliving surfaces and are known to mediate a broad range of processes in ecology, medicine, and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using molecular dynamics simulations and continuous modeling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with a free boundary and demonstrate that such an expanding colony self-organizes into a "mosaic" of mic…
The near-surface swimming patterns of bacteria are strongly determined by the hydrodynamic interactions between bacteria and the surface, which trap bacteria in smooth circular trajectories that lead to inefficient surface exploration. Here, we show by combining experiments and a data-driven mathematical model that surface exploration of enterohemorrhagic Escherichia coli (EHEC) -- a pathogenic strain of E. coli causing serious illnesses such as bloody diarrhea -- results from a complex interplay between motility and transient surface adhesion events. These events allow EHEC to break the smoot…
We study the spreading of a bacterial colony undergoing turbulent like collective motion. We present two minimalistic models to investigate the interplay between population growth and coherent structures arising from turbulence. Using Direct Numerical Simulation (DNS) of the proposed models we find that turbulence has two prominent effects on the spatial growth of the colony: (a) the front speed is enhanced, and (b) the front gets crumpled. Both these effects, which we highlight by using statistical tools, are markedly different in our two models. We also show that the crumpled front structure…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body which is propelled by a force-free mechanism. To account for the behavior of living bacteria, the model also incorporates a run-and-tumble process. The model bacteria are capable of hydrodynamically interacting with both of the channel walls and the obstacle. This enables the bacteria to get reoriented when experiencing a shear-flow. We demonstrate that this mod…
We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape with the dynamics of growth and constriction. The model allows us to derive constraints on cell wall mechanical energy based on the observed dynamics of cell shape. We predict that exponential growth in cell size requires a constant amount of cell wall energy to be dissipated per unit volume. We use the model to understand and contrast growth in bacteria with …
Colloids coupled to a bath of swimming cells generically display enhanced diffusion. This transport dynamics stems from a subtle interplay between the active and passive particles that still resists our understanding despite decades of intense research. Here, we tackle the root of the problem by providing a quantitative characterisation of the single scattering events between a colloid and a bacterium. Based on our experiments, we build a minimal model that quantitatively predicts the geometry of the scattering trajectories, and enhanced colloidal diffusion at long times. This quantitative con…
Viral fibers play a central role in many virus infection mechanisms since they recognize the corresponding host and establish a mechanical link to its surface. Specifically, bacteriophages have to anchor to bacteria through the fibers surrounding the tail before starting the viral DNA translocation into the host. The protein gene product (gp) 37 from bacteriophage T4 long tail fibers forms a fibrous parallel homotrimer located at the distal end of the long tail fibers. Biochemical data indicate that, at least three of these fibers are required for initial host cell interaction, but do not reve…
In purple bacteria, the fundamental charge-separation step that drives the conversion of radiation energy into chemical energy proceeds along one branch - the A branch - of a heterodimeric pigment-protein complex, the reaction center. Here, we use first principles time-dependent density functional theory (TDDFT) with an optimally-tuned range-separated hybrid functional to investigate the electronic and excited-state structure of the primary six pigments in the reaction center of \textit{Rhodobacter sphaeroides}. By explicitly including amino-acid residues surrounding these six pigments in our …
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous symmetry-breaking or might be triggered by external signals and preexisting asymmetries, e.g. through a previous septation in bacteria. Although very complex, a key feature of cellular motility is the ability of actin to form dense polymeric networks, whose microstructure is tightly regulated by the cell. These polar actin networks produce the forces necessary for…
Electronic 2D spectroscopy allows nontrivial quantum effects in chemistry and biology to be explored in unprecedented detail. Here, we apply recently developed fluorescence detected coherent 2D spectroscopy to study the light harvesting antenna 2 (LH2) of photosynthetic purple bacteria. The method utilizes the destructive interference between two signal components thereby uncovering cross peaks which are not visible in conventional photon-echo based 2D and transient absorption measurements. Analyses of signal generating quantum pathways leads to the conclusion that, contrary to the currently p…
Excitation transfer through interacting systems plays an important role in many areas of physics, chemistry, and biology. The uncontrollable interaction of the transmission network with a noisy environment is usually assumed to deteriorate its transport capacity, especially so when the system is fundamentally quantum mechanical. Here we identify key mechanisms through which noise such as dephasing, perhaps counter intuitively, may actually aid transport through a dissipative network by opening up additional pathways for excitation transfer. We show that these are processes that lead to the inh…
Topological signatures of collective dynamics and turbulent-like energy cascades in apolar active granular
School of Physics and Astronomy, Shanghai Jiao Tong University（上海交通大学物理与天文学院）；Institute of Natural Sciences, Shanghai Jiao Tong University（上海交通大学自然科学研究院）；Wilczek Quantum Center, School of Physics and Astronomy, Shanghai Jiao Tong University（上海交通大学物理与天文学院吴文俊物理学中心）；Shanghai Research Center for Quantum Sciences（上海量子科学研究中心）
