"… We examine here how the algorithm of phyllotaxis could contribute to the analysis of the structure of collagen fibrils. Such an algorithm indeed leads to organizations giving to each element of the assembly the most homogeneous and isotropic dense environment in a situation of cylindrical symmetry. The scattered intensity expected from a phyllotactic distribution of triple helices in collagen fibrils well agrees with the major features observed along the equatorial direction of their X ray patterns. Following this approach, the aggregation of triple helices in fibrils should be considered within the frame of soft condensed matter studies rather than that of molecular crystal studies."

"We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths of these interactions. When the nonspecific interaction is strong, liquidlike clustering can precede crystallization; when it is weak, growth can proceed via ordered nuclei. Crystal yields are in certain parameter regimes enhanced by the nonspecific interaction, even though it promotes association without local crystalline order. Our results suggest that equipping nanoscale components with weak nonspecific interactions (such as depletion attractions) can alter both their dynamical pathway of assembly and optimize the yield of the resulting material."

"The possibility of microscopic swimming by extraction of energy from an external flow is discussed, focusing on the migration of a simple trimer across a linear shear flow. The geometric properties of swimming, together with the possible generalization to the case of a vesicle, are analyzed.The mechanism of energy extraction from the flow appears to be the generalization to a discrete swimmer of the tank-treading regime of a vesicle. The swimmer takes advantage of the external flow by both extracting energy for swimming and "sailing" through it. The migration velocity is found to scale linearly in the stroke amplitude, and not quadratically as in a quiescent fluid. This effect turns out to be connected with the non-applicability of the scallop theorem in the presence of external flow fields."

"How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions between their proteins? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in crowded cellular environment. The model cell includes three independent pathways, whose topologies of PPI subnetworks are different, but whose functional concentrations equally contribute to cell's fitness. The model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical-chemical properties of protein interactions and their abundances due to a "frustration" effect: strengthening of functional interactions brings about hydrophobic surfaces, which make proteins prone to promiscuous binding.…"

"…Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. In contrast to the commonly held view, we show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement comes about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signalling systems."

"Genetic oscillators are a major theme of interest in the emerging field of synthetic biology. Until recently, most work has been carried out using intra-cellular oscillators, but this approach restricts the broader applicability of such systems. Motivated by a desire to develop large-scale, spatially-distributed cell-based computational systems, we present an initial design for a population-level oscillator which uses three different bacterial strains. Our system is based on the client-server model familiar to computer science, and uses quorum sensing for communication between nodes. We present the results of extensive in silico simulation tests, which confirm that our design is both feasible and robust."

"This paper introduces the theory and practice of formal verification of self-assembling systems. We interpret a well-studied abstraction of nanomolecular self assembly, the Abstract Tile Assembly Model (aTAM), into Computation Tree Logic (CTL), a temporal logic often used in model checking. We then consider the class of "rectilinear" tile assembly systems. This class includes most aTAM systems studied in the theoretical literature, and all (algorithmic) DNA tile self-assembling systems that have been realized in laboratories to date. We present a polynomial-time algorithm that, given a tile assembly system T as input, either provides a counterexample to T's rectilinearity or verifies whether T has a unique terminal assembly. …"