35 Result(s)
within
Alfonso Rodríguez-Patón
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Article
A Parallel Image Skeletonizing Method Using Spiking Neural P Systems with Weights
Spiking neural P systems (namely SN P systems, for short) are bio-inspired neural-like computing models under the framework of membrane computing, which are also known as a new candidate of the third generatio...
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Article
Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations
Targeted killing of pathogenic bacteria without harming beneficial members of host microbiota holds promise as a strategy to cure disease and limit both antimicrobial-related dysbiosis and development of antim...
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Article
Preface
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Chapter
An Implementation of Elementary Arithmetic with Virus Machine
In recent years, the popularity of natural computing has been on the increase. Recently, it has inspired a novel biological computational model, called virus machine, which incorporates concepts from virology ...
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Article
Open AccessProbability-based collaborative filtering model for predicting gene–disease associations
Accurately predicting pathogenic human genes has been challenging in recent research. Considering extensive gene–disease data verified by biological experiments, we can apply computational methods to perform a...
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Article
Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments
Recent links between computer science and synthetic biology allow for construction of many kinds of algorithmic processes within cells, obtained either by a direct engineered design or by an evolutionary searc...
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Chapter and Conference Paper
A Preliminary Assessment of Three Strategies for the Agent-Based Modeling of Bacterial Conjugation
Bacterial conjugation is a cell-cell communication by which neighbor cells transmit circular DNA strands called plasmids. The transmission of these plasmids has been traditionally modeled using differential eq...
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Chapter and Conference Paper
BactoSim – An Individual-Based Simulation Environment for Bacterial Conjugation
BactoSim is an agent-based platform for simulating the conjugation in spatially structured bacterial populations, which are the conditions typically found on naturally occurring colonies such as biofilms or in...
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Article
Probabilistic reasoning with a Bayesian DNA device based on strand displacement
We present a computing model based on the DNA strand displacement technique, which performs Bayesian inference. The model will take single-stranded DNA as input data, that represents the presence or absence of...
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Chapter and Conference Paper
Probabilistic Reasoning with an Enzyme-Driven DNA Device
We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DN...
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Chapter and Conference Paper
Probabilistic Reasoning with a Bayesian DNA Device Based on Strand Displacement
We present a computing model based on the DNA strand displacement technique which performs Bayesian inference. The model will take single stranded DNA as input data, representing the presence or absence of a s...
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Chapter and Conference Paper
Distributed Computing with Prokaryotic Immune Systems
Summary: We propose the in vivo/vitro use of prokaryotic adaptive immune systems for distributed learning. In the coming years synthetic biologists will learn to control, program, and mod...
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Article
A review of the nondeterministic waiting time algorithm
We provide the description for the nondeterministic waiting time (NWT) algorithm, a biochemical modeling approach based on the membrane systems paradigm of computation. The technique provides a unique (differe...
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Chapter and Conference Paper
Simulating a Rock-Scissors-Paper Bacterial Game with a Discrete Cellular Automaton
This paper describes some of the results obtained after the design and implementation of a discrete cellular automata simulating the generation, degradation and diffusion of particles in a two dimensional grid...
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Chapter and Conference Paper
Polynomial Complexity Classes in Spiking Neural P Systems
We study the computational potential of spiking neural (SN) P systems. several intractable problems have been proven to be solvable by these systems in polynomial or even constant time. We study first their fo...
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Chapter and Conference Paper
Autonomous Resolution Based on DNA Strand Displacement
We present a computing model based on the technique of DNA strand displacement which performs a chain of logical resolutions with logical formulae in conjunctive normal form. The model is enzyme-free and auton...
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Chapter and Conference Paper
Inference with DNA Molecules
We have designed a simple model that implement the inference rules Modus Ponens and Modus Tollens using DNA. The model is inspired by [1,2], but implemented using DNA strand displacement as a reinterpretation of ...
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Chapter and Conference Paper
On the Power of Computing with Proteins on Membranes
P systems with proteins on membranes are inspired closely by switching protein channels. This model of membrane computing using membrane division has been previously shown to solve an NP-complete problem in po...
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Chapter and Conference Paper
Sequentiality Induced by Spike Number in SNP Systems
The spiking neural P systems are a class of computing devices recently introduced as a bridge between spiking neural nets and membrane computing. In this paper we consider sequential SNP systems where the sequ...
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Chapter and Conference Paper
A New Model of Synthetic Genetic Oscillator Based on Trans-Acting Repressor Ribozyme
We present a new model of synthetic genetic oscillator based on a typical motif with one positive and one negative feedback loop. The repressor is a ribozyme, rather than a protein, which acts post-transcripti...
