Related papers: The Computational Universality of Metabolic Comput…

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…

One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…

The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…

Characterising the intelligence of biological organisms is challenging. This work considers intelligent algorithms developed evolutionarily within neural systems. Mathematical analyses unveil a natural equivalence between canonical neural…

So far, following the works of A.M. Turing, the algorithms were considered as the mathematical abstraction from which we could write programs for computers whose principle was based on the theoretical concept of Turing machine. We start…

A new model for mechanical computing is demonstrated that requires only two basic parts: links and rotary joints. These basic parts are combined into two main higher level structures: locks and balances, which suffice to create all…

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…

The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…

This work exposes which mechanisms and procesess in the Nature of evolution compute a function not computable by Turing machine. The computer with intelligence that is not higher than one bacteria population could have, but with efficency…

Evolutionary processes proved very useful for solving optimization problems. In this work, we build a formalization of the notion of cooperation and competition of multiple systems working toward a common optimization goal of the population…

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…

We study the problem of determining whether a given temporal specification can be implemented by a symmetric system, i.e., a system composed from identical components. Symmetry is an important goal in the design of distributed systems,…

Whether P systems with only one catalyst can already be computationally complete, is still an open problem. Here we establish computational completeness by using specific variants of additional control mechanisms. At each step using only…

Predicting cellular metabolic states is a central problem in biophysics. Conventional approaches, however, sensitively depend on the microscopic details of individual metabolic systems. In this Letter, we derived a universal linear…

Adiabatic quantum computation has recently attracted attention in the physics and computer science communities, but its computational power was unknown. We describe an efficient adiabatic simulation of any given quantum algorithm, which…

Formal methods apply algorithms based on mathematical principles to enhance the reliability of systems. It would only be natural to try to progress from verification, model checking or testing a system against its formal specification into…

Building software-driven systems that are easily understood becomes a challenge, with their ever-increasing complexity and autonomy. Accordingly, recent research efforts strive to aid in designing explainable systems. Nevertheless, a common…

Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…

A general condition determining the optimal performance of a complex system has not yet been found and the possibility of its existence is unknown. To contribute in this direction, an optimization algorithm as a complex system is presented.…