Life at the edge: Complexity and criticality in biological function

Why life is complex and - most importantly - what is the origin of the over abundance of complexity in nature? This is a fundamental scientific question which, paraphrasing the late Per Bak, “is screaming to be answered but seldom is even being asked”. In this article, we review recent attempts across several scales to understand the origins of complex biological problems from the perspective of critical phenomena. To illustrate the approach, three cases are discussed, namely the large scale brain dynamics, the characterization of spontaneous fluctuations of proteins, and the physiological complexity of the cell mitochondria network.Fil: Chialvo, Dante Renato. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentin

Brain complexity born out of criticality

In this essay we elaborate on recent evidence demonstrating the presence of a second order phase transition in human brain dynamics and discuss its consequences for theoretical approaches to brain function. We review early evidence of criticality in brain dynamics at different spatial and temporal scales, and we stress how it was necessary to unify concepts and analysis techniques across scales to introduce the adequate order and control parameters which define the transition. A discussion on the relation between structural vs. dynamical complexity exposes future steps to understand the dynamics of the connectome (structure) from which emerges the cognitome (function).Comment: In Proceedings of the 12th Granada Seminar "Physics, Computation, and the Mind - Advances and Challenges at Interfaces-". (J. Marro, P. L. Garrido & J. J. Torres, Eds.) American Institute of Physics (2012, in press

On the molecular mechanism of surface charge amplification and related phenomena at aqueous polyelectrolyte-graphene interfaces

In this communication we illustrate the occurrence of a recently reported new phenomenon of surface-charge amplification, SCA, (originally dubbed overcharging, OC), [Jimenez-Angeles F. and Lozada-Cassou M., J. Phys. Chem. B, 2004, 108, 7286] by means of molecular dynamics simulation of aqueous electrolytes solutions involving multivalent cations in contact with charged graphene walls and the presence of short-chain lithium polystyrene sulfonates where the solvent water is described explicitly with a realistic molecular model. We show that the occurrence of SCA in these systems, in contrast to that observed in primitive models, involves neither contact co-adsorption of the negatively charged macroions nor divalent cations with a large size and charge asymmetry as required in the case of implicit solvents. In fact the SCA phenomenon hinges around the preferential adsorption of water (over the hydrated ions) with an average dipolar orientation such that the charges of the water's hydrogen and oxygen sites induce magnification rather than screening of the positive-charged graphene surface, within a limited range of surface-charge density.Comment: 10 pages, 6 figure

Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method

An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition approach to accelerate the neighbor list construction speed, and data sorting method to lower the CPU data cache miss rate, as well as partial updating method to minimize the unnecessary reconstruction of the neighbor list. Both serial and parallel performance of molecular dynamics simulation are evaluated using the proposed algorithm and compared with those using conventional Verlet table and cell linked list algorithms. Results show that the new algorithm outperforms the conventional algorithms by a factor of 2~3 in cases of both small and large number of atoms.Comment: 14 pages, 7 figures. Submitted to Computer Physics Communication