Biomedical subjects

R Lahoz-Beltra

Publications and source records attributed to R Lahoz-Beltra.

4 recordsLinked to original sources

PubMed2001

Evolving hardware as model of enzyme evolution.

Organism growth and survival is based on thousands of enzymes organized in networks. The motivation to understand how a large number of enzymes evolved so fast inside cells may be relevant to explaining the origin and maintenance of life on Earth. This paper presents electronic circuits called 'electronic enzymes' that model the catalytic function performed by biological enzymes. Electronic enzymes are the hardware realization of enzymes defined as molecular automata with a finite number of internal conformational states and a set of Boolean operators modelling the active groups of the active site. One of the main features of electronic enzymes is the possibility of evolution finding the proper active site by means of a genetic algorithm yielding a metabolic ring or k-cycle that bears a resemblance to Krebs (k=7) or Calvin (k=4) cycles present in organisms. The simulations are consistent with those results obtained in vitro evolving enzymes based on polymerase chain reaction (PCR) as well as with the general view that suggests the main role of recombination during enzyme evolution. The proposed methodology shows how molecular automata with evolvable features that model enzymes or other processing molecules provide an experimental framework for simulation of the principles governing metabolic pathways evolution and self-organization.

Algorithms↗

PubMed1997

Molecular automata assembly: principles and simulation of bacterial membrane construction.

The motivation to understand the basic rules and principles governing molecular self-assembly may be relevant to explain in the context of molecular biology the self-organization and biological functions exhibited within cells. This paper presents a molecular automata model to simulate molecular self-assembly introducing the concept of molecular programming to simulate the biological function or operation performed by an assembled molecular state machine. The method is illustrated modelling Escherichia coli membrane construction including the assembly and operation of ATP synthase as well as the assembly of the bacterial flagellar motor. Flagellar motor operation was simulated using a different approach based on state machine definition used in virtual reality systems. The proposed methodology provides a modelling framework for simulation of biological functions performed by cellular components and other biological systems suitable to be modelled as molecular state machines.

Algorithms↗

PubMed1994

Cytoskeletal involvement in neuronal learning: a review.

This paper introduces the ideas of neural networks in the context of currently recognized cellular structures within neurons. Neural network models and paradigms require adaptation of synapses for learning to occur in the network. Some models of learning paradigms require information to move from axon to dendrite. This motivated us to examine the possibility of intracellular signaling to mediate such signals. The cytoskeleton forms a substrate for intracellular signaling via material transport and other putative mechanisms. Furthermore, many experimental results suggest a link between the cytoskeleton and cognitive processing. In this paper we review research on intracellular signaling in the context of neural network learning.

Animals↗

PubMed1993

Cytoskeletal logic: a model for molecular computation via Boolean operations in microtubules and microtubule-associated proteins.

Adaptive behaviors and dynamic activities within living cells are organized by the cytoskeleton: intracellular networks of interconnected protein polymers which include microtubules (MTs), actin, intermediate filaments, microtubule associated proteins (MAPs) and other protein structures. Cooperative interactions among cytoskeletal protein subunit conformational states have been used to model signal transmission and information processing. In the present work we present a theoretical model for molecular computing in which Boolean logic is implemented in parallel networks of individual MTs interconnected by MAPs. Conformational signals propagate on MTs as in data buses and in the model MAPs are considered as Boolean operators, either as bit-lines (like MTs) where a signal can be transported unchanged between MTs ('BUS-MAP'), or as bit-lines where a Boolean operation is performed in one of the two MAP-MT attachments ('LOGIC-MAP'). Three logic MAPs have been defined ('NOT-MAP, 'AND-MAP', 'XOR-MAP') and used to demonstrate addition, subtraction and other arithmetic operations. Although our choice of Boolean logic is arbitrary, the simulations demonstrate symbolic manipulation in a connectionist system and suggest that MT-MAP networks can perform computation in living cells and are candidates for future molecular computing devices.

Animals↗