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We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent. Our theory reveals the existence of an intermediate situation between ionic and covalent which may be almost barrierless and isoenegetic and which should be of high interest for understanding biochemistry.
A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE will be a true breakthrough in description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. The revolutionary ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine specimen from the created numerous truncated constructs of UDE were choosen to dechiper structural and functional relationships. VUVCD with neural network was performed to define the secondary structure content and location of UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Partition of α-helical boundles comparison with the truncated protein segments denoted new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues in pupating insects. Here we demonstrate that combination of ESPRIT and VUVCD with NN provided significant structural description of UDE and resulted useful truncated constructs for further detailed functional studies.
The role of neuro-inflammation in diverse, acute and chronic brain pathologies is being increasingly recognized. Neuro-inflammation is accompanied by increased levels of both pro- and anti-inflammatory cytokines; these have deleterious as well as protective/reparative effects. Inflammation has varying effects on neurogenesis and is a subject of intense contemporary interest. We show that TNF-alpha and IFN-gamma, used concomitantly, cause apoptosis of adult rat hippocampal progenitor/stem cells in vitro as detected by the TUNEL and MTT assays on time scales of several hours. We have coupled Raman spectroscopy to an optical trap to probe early changes of apoptosis in single, live neural stem cells that have been treated with pro-inflammatory cytokines, TNF-alpha and IFN-gamma. Changes caused by inflammation-induced denaturation of DNA are observed in the Raman spectra that correspond to very early stages of apoptosis, occurring on very fast time scales: as short as 10 minutes. Addition of the anti-inflammatory cytokine IL-10 either 10-30 min before or 10-30 min after treatment with TNF-alpha and IFN-gamma reverses the changes substantially. Our findings imply that inflammation can induce very rapid changes leading to cell death but that these are reversible, in the early stages at least.
In Dictyostelium discoideum the proportion of cell types is known to be actively regulated, recovering, for example, after the removal of a given cell type. However, we have recently shown that regulation is intrinsically imprecise: it controls the proportion above/below certain upper and lower thresholds, but not within an allowed range of values that these thresholds define. To explain this finding we present a model based on (i) a global negative feedback, and (ii) a cell-autonomous positive feedback leading to a hysteresis-like behaviour (i.e, a bistability of cell type). The simulated cell-type proportion is indeed found to span a range of values as a consequence of the bistability. We conclude that there is a general conflict between the precision of proportion regulation and the robustness of the differentiation of cell types.
We report a theoretical/computational approach for modeling the current-voltage characteristics of sensing proteins. The modeling is applied to a couple of transmembrane proteins, bacteriorhodopsin and proteorhodopsin, sensitive to visible light and promising biomaterials for the development of a new generation of photo-transducers. The agreement between theory and experiments sheds new light on the microscopic interpretation of charge transfer in proteins and biological materials in general.
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for an intermediate period between collective fixed-point behavior. The control mechanism works by monotonically increasing a single bifurcation parameter. Both the onset and arrest of oscillations are due to bifurcations. Depending on the coupling strength, the network topology and the tuning speed, our numerical simulations reveal a rich dynamics out-of-equilibrium with multiple inherent time scales, long transients towards the stationary states and interesting transient patterns like self-organized pacemakers. Zooming into the transition regime, we pursue the arrest of oscillations along the arms of spirals. We point out possible relations to the genetic network of segmentation clocks.
ATP-binding cassette (ABC) transporters are integral membrane proteins that mediate the exchange of diverse substrates across membranes powered by ATP hydrolysis. We report results of coarse-grained dynamical simulations performed for the bacterial heme transporter HmuUV. Based on the nucleotide-free structure, we have constructed a ligand-elastic-network description for this protein and investigated ATP-induced conformational motions in structurally resolved computer experiments. As we found, interactions with nucleotides resulted in generic motions which are functional and robust. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact and the transmembrane domains were rotated. The heme channel was broadened in the ligand-bound complex and the gate to the cytoplasm, which was closed in the nucleotide-free conformation, was rendered open by a mechanism that involved tilting motions of essential transmembrane helices. Based on our findings we propose that the HmuUV transporter behaves like a `simple' mechanical device in which, induced by binding of ATP ligands, linear motions of the nucleotide-binding domains are translated into rotational motions and internal tilting dynamics of the transmembrane domains that control gating inside the heme pathway.
Memristors have been suggested as neuromorphic computing elements. Spike-time dependent plasticity and the Hodgkin-Huxley model of the neuron have both been modelled effectively by memristor theory. The d.c. response of the memristor is a current spike. Based on these three facts we suggest that memristors are well-placed to interface directly with neurons. In this paper we show that connecting a spiking memristor network to spiking neuronal cells causes a change in the memristor network dynamics by: removing the memristor spikes, which we show is due to the effects of connection to aqueous medium; causing a change in current decay rate consistent with a change in memristor state; presenting more-linear $I-t$ dynamics; and increasing the memristor spiking rate, as a consequence of interaction with the spiking neurons. This demonstrates that neurons are capable of communicating directly with memristors, without the need for computer translation.
I propose to treat the biological evolution of genoms by means of quantum mechanical tools. We start with the concept of meta- gene, which specifies the "selfish gene" of R.Dawkins. Meta- gene encodes the abstract living unity, which can live relatively independently of the others, and can contain a few real creatures. Each population of living creatures we treat as the wave function on meta- genes, which module squared is the total number of creatures with the given meta-gene, and the phase is the sum of "aspirations" to change the classical states of meta- genes. Each individual life thus becomes one of possible outcomes of the virtual quantum measurement of this function. The evolution of genomes is described by the unitary operator in the space of psi-functions or by Kossovsky-Lindblad equation in the case of open biosystems. This operator contains all the information about specific conditions under which individuals are, and how "aspirations" of their meta- genes may be implemented at the biochemical level. We show the example of quantum description of the population with two parts of meta-gene: "wolves" and "deer", which can be simultaneously in the same abstract living unity. "Selfish gene" reconciled with the notion of individuality of alive beings that gives possibility to consider evolutionary scenarios and their possible physical causes from the single position.
Gliding of microtubule filaments on surfaces coated with the motor protein kinesin has potential applications for nano-scale devices. The ability to guide the gliding direction in three dimensions allows the fabrication of tracks of arbitrary geometry in space. Here, we achieve this by using kinesin-coated glass wires of micrometer diameter range. Unlike previous methods in which the guiding tracks are fixed on flat two-dimensional surfaces, the flexibility of glass wires in shape and size facilitates building in-vitro devices that have deformable tracks.
Single and collective cellular oscillations involving the actomyosin cytoskeleton have been observed in numerous biological systems. We show here that a generic model of a contractile material, which is turning over and contracts against an elastic element, exhibits spontaneous oscillations. Such a model can thus account for shape oscillations observed in amnioserosa cells during dorsal closure of the Drosophila embryo. We investigate the collective dynamics of an ensemble of such oscillators and show that the relative contribution of viscous and friction losses yield different regimes of collective oscillations. Taking into account the diffusion of contractile elements, our theoretical framework predicts the appearance of traveling waves which might account for the propagation of actomyosin contractile waves observed during morphogenesis.
This work asks how light harvesting in photosynthetic systems can be optimised for economically scalable, sustainable energy production. Hierarchy theory is introduced as a system-analysis and optimisation tool better able to handle multiscale, multiprocess complexities in photosynthetic energetics compared with standard linear-process analysis. Within this framework, new insights are given into relationships between composition, structure and energetics at the scale of the thylakoid membrane, and also into how components at different scales cooperate under functional objectives of the whole photosynthetic system. Combining these reductionistic and holistic analyses creates a platform for modelling multiscale-optimal, idealised photosynthetic systems in silico.
The supply of oxygen and nutrients and the disposal of metabolic waste in the organs depend strongly on how blood, especially red blood cells, flow through the microvascular network. Macromolecular plasma proteins such as fibrinogen cause red blood cells to form large aggregates, called rouleaux, which are usually assumed to be disaggregated in the circulation due to the shear forces present in bulk flow. This leads to the assumption that rouleaux formation is only relevant in the venule network and in arterioles at low shear rates or stasis. Thanks to an excellent agreement between combined experimental and numerical approaches, we show that despite the large shear rates present in microcapillaries, the presence of either fibrinogen or the synthetic polymer dextran leads to an enhanced formation of robust clusters of red blood cells, even at haematocrits as low as 1%. Robust aggregates are shown to exist in microcapillaries even for fibrinogen concentrations within the healthy physiological range. These persistent aggregates should strongly affect cell distribution and blood perfusion in the microvasculature, with putative implications for blood disorders even within apparently asymptomatic subjects.
We adopt the so--called \emph{occupation number representation}, originally used in quantum mechanics and recently adopted in the description of several classical systems, in the analysis of the dynamics of some models of closed ecosystems. In particular, we discuss two linear models, for which the solution can be found analytically, and a nonlinear system, for which we produce numerical results. We also discuss how a damping effect could be {\em effectively} implemented in the model.
We simulate a model of self-propelled disks with soft repulsive interactions confined to a box in two dimensions. For small rotational diffusion rates, monodisperse disks spontaneously accumulate at the walls. At low densities, interaction forces between particles are strongly inhomogeneous, and a simple model predicts how these inhomogeneities alter the equation of state. At higher densities, collective effects become important. We observe signatures of a jamming transition at a packing fraction $ϕ\sim 0.88$, which is also the jamming point for non-active athermal monodisperse disks. At this $ϕ$, the system develops a critical finite active speed necessary for wall aggregation. At packing fractions above $ϕ\sim 0.6$, the pressure decreases with increasing density, suggesting that strong interactions between particles are affecting the equation of state well below the jamming transition. A mixture of bidisperse disks segregates in the absence of any adhesion, identifying a new mechanism that could contribute to cell sorting in embryonic development.
Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both sense and generate local membrane curvature. Here we investigate through Dynamical Triangulation Monte Carlo simulations, the role that these active processes play in determining the morphology and compositional segregation in closed membranes. Our results suggest that the ramified morphologies of organelles observed in-vivo are a consequence of driven nonequilibrium processes rather than equilibrium forces.
We describe the effect of optical aberrations on fluorescence fluctuations microscopy (FFM), when focusing through a single living cell. FFM measurements are performed in an aqueous fluorescent solution and prove to be a highly sensitive tool to assess the optical aberrations introduced by the cell. We demonstrate an adaptive optics (AO) system to remove the aberration-related bias in the FFM measurements. Our data show that AO is not only useful when imaging deep in tissues but also when performing FFM measurements through a single cellular layer. This work paves the way for the application of FFM to complex three-dimensional multicellular samples.
We propose a minimal model of predator-swarm interactions which captures many of the essential dynamics observed in nature. Different outcomes are observed depending on the predator strength. For a "weak" predator, the swarm is able to escape the predator completely. As the strength is increased, the predator is able to catch up with the swarm as a whole, but the individual prey are able to escape by "confusing" the predator: the prey forms a ring with the predator at the center. For higher predator strength, complex chasing dynamics are observed which can become chaotic. For even higher strength, the predator is able to successfully capture the prey. Our model is simple enough to be amenable to a full mathematical analysis which is used to predict the shape of the swarm as well as the resulting predator-prey dynamics as a function of model parameters. We show that as the predator strength is increased, there is a transition (due to a Hopf bifurcation) from confusion state to chasing dynamics, and we compute the threshold analytically. Our analysis indicates that the swarming behaviour is not helpful in avoiding the predator, suggesting that there are other reasons why the species may swarm. The complex shape of the swarm in our model during the chasing dynamics is similar to the shape of a flock of sheep avoiding a shepherd.