Atsushi Kamimura

Reproduction of a protocell by replication of a minority molecule in a catalytic reaction network.

For understanding the origin of life, it is essential to explain the development of a compartmentalized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that mutually catalyze each other is considered in order to show that the reproduction of a protocell with a growth-division process naturally occurs when the replication speed of one chemical is considerably slower than that of the other chemical, and molecules are crowded as a result of replication. It is observed that the protocell divides after a minority molecule is replicated at a slow synthesis rate, and thus, a synchrony between the reproduction of a cell and molecule replication is achieved. The robustness of such protocells against the invasion of parasitic molecules is also demonstrated.

Dynamics of intracellular information decoding

A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity.

Group chase and escape with conversion from targets to chasers

We study the effect of converting caught targets into new chasers in the context of the recently proposed ‘group chase and escape’ problem. Numerical simulations have shown that this conversion can substantially reduce the lifetimes of the targets when a large number of them are initially present. At the same time, it also leads to a non-monotonic dependence on the initial number of targets, resulting in the existence of a maximum lifetime. As a counter-effect for this conversion, we further introduce self-multiplying abilities to the targets. We found that the longest lifetime exists when a suitable combination of these two effects is created.

Theoretical Aspects of Cellular Decision-Making and Information-Processing

Microscopic biological processes have extraordinary complexity and variety at the sub-cellular, intra-cellular, and multi-cellular levels. In dealing with such complex phenomena, conceptual and theoretical frameworks are crucial, which enable us to understand seemingly different intra- and inter-cellular phenomena from unified viewpoints. Decision-making is one such concept that has attracted much attention recently. Since a number of cellular behavior can be regarded as processes to make specific actions in response to external stimuli, decision-making can cover and has been used to explain a broad range of different cellular phenomena [Balázsi et al. (Cell 144(6):910, 2011), Zeng et al. (Cell 141(4):682, 2010)]. Decision-making is also closely related to cellular information-processing because appropriate decisions cannot be made without exploiting the information that the external stimuli contain. Efficiency of information transduction and processing by intra-cellular networks determines the amount of information obtained, which in turn limits the efficiency of subsequent decision-making. Furthermore, information-processing itself can serve as another concept that is crucial for understanding of other biological processes than decision-making. In this work, we review recent theoretical developments on cellular decision-making and information-processing by focusing on the relation between these two concepts.

Compartmentalization and Cell Division through Molecular Discreteness and Crowding in a Catalytic Reaction Network

Explanation of the emergence of primitive cellular structures from a set of chemical reactions is necessary to unveil the origin of life and to experimentally synthesize protocells. By simulating a cellular automaton model with a two-species hypercycle, we demonstrate the reproduction of a localized cluster; that is, a protocell with a growth-division process emerges when the replication and degradation speeds of one species are respectively slower than those of the other species, because of overcrowding of molecules as a natural outcome of the replication. The protocell exhibits synchrony between its division process and replication of the minority molecule. We discuss the effects of the crowding molecule on the formation of primitive structures. The generality of this result is demonstrated through the extension of our model to a hypercycle with three molecular species, where a localized layered structure of molecules continues to divide, triggered by the replication of a minority molecule at the center.

Visuomotor Tracking Tasks With Delayed Pursuit and Escape

Virtual stick balancing (VSB) is a manual visuomotor tracking task that involves interplay between a human and a computer in which the movements are programmed to resemble those of balancing a stick at the fingertip. Since time delays and random perturbations (“noise”) are intrinsic properties of this task, we modeled VSB as a delayed pursuit-escape process: the target movements are described by a simple random walk and those movements controlled by the computer mouse by a delayed random walk biased towards the target. As subjects become more skilled, a stereotyped and recurring pursuit‐escape pattern develops in which the mouse pursues the target until it overtakes it, causing the target to move in a different direction, followed, after a lag, by the pursing mouse. The delayed pursuit-escape random walk model captured the qualitative nature of this tracking task and provided insights into why this tracking task always fails at some point in time, even for the most expert subjects.

Negative scaling relationship between molecular diversity and resource abundances.

Cell reproduction involves replication of diverse molecule species, in contrast to a simple replication system with fewer components. To address this question of diversity, we study theoretically a cell system with catalytic reaction dynamics that grows by uptake of environmental resources. It is shown that limited resources lead to increased diversity of components within the system, and the number of coexisting species increases with a negative power of the resource uptake. The relationship is explained from the optimum growth speed of the cell, determined by a tradeoff between the utility of diverse resources and the concentration onto fewer components to increase the reaction rate.

Stochastic resonance with group chase and escape

We describe a simple model developed under the new idea of one group chasing another called, “group chase and escape”. We will demonstrate that even a simple model can exhibit rather rich and complex behavior. In particular, we show that the appropriate level of fluctuation in each step of the process for chase and escape can minimize the time taken for the entire catch.

Information Processing and Integration with Intracellular Dynamics Near Critical Point

Recent experimental observations suggest that cells can show relatively precise and reliable responses to external signals even though substantial noise is inevitably involved in the signals. An intriguing question is the way how cells can manage to do it. One possible way to realize such response for a cell is to evolutionary develop and optimize its intracellular signaling pathways so as to extract relevant information from the noisy signal. We recently demonstrated that certain intracellular signaling reactions could actually conduct statistically optimal information processing. In this paper, we clarify that such optimal reaction operates near bifurcation point. This result suggests that critical-like phenomena in the single-cell level may be linked to efficient information processing inside a cell. In addition, improving the performance of response in the single-cell level is not the only way for cells to realize reliable response. Another possible strategy is to integrate information of individual cells by cell-to-cell interaction such as quorum sensing. Since cell-to-cell interaction is a common phenomenon, it is equally important to investigate how cells can integrate their information by cell-to-cell interaction to realize efficient information processing in the population level. In this paper, we consider roles and benefits of cell-to-cell interaction by considering integrations of obtained information of individuals with the other cells from the viewpoint of information processing. We also demonstrate that, by introducing cell movement, spatial organizations can spontaneously emerge as a result of efficient responses of the population to external signals.

Dynamical aspect of group chase and escape

Recently, a new concept is proposed for chasing and evading in crowds, called “group chase and escape” through a simple model. In this model, two kinds of players, chasers and escapees, play tag on a two‐dimensional square lattice. Each chaser approaches its nearest escapee. On the other hand, each escapee steps away from its nearest chaser. Although there are no communications within each group, players appear to cooperate among themselves to chase or escape. We found relation between this cooperative behavior and group formations depend on the density of chasers and targets.