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DNA Sequencing via Quantum Mechanics and Machine Learning
DNA Sequencing Quantum Mechanics Machine Learning
2011/1/5
Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a sol...
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
ADAM Analysis of Discrete Models
2011/1/5
Motivation: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, bounded Petri nets, and agent-based models. Simulation is a ...
Thermal soaring flight of birds and unmanned aerial vehicles
Thermal soaring flight of birds unmanned aerial vehicles
2011/1/5
Thermal soaring saves much energy, but flying large distances in this form represents a great challenge for birds, people and Unmanned Aerial Vehicles (UAVs). The solution is to make use of so-called ...
Information theoretic interpretation of frequency domain connectivity measures
Information theoretic interpretation frequency domain connectivity measures
2011/1/5
To provide adequate multivariate measures of information flow between neural structures, modified expressions of Partial Directed Coherence (PDC) and Directed Transfer Function (DTF), two popular mult...
Delayed feedback causes non-Markovian behavior of neuronal firing statistics
Delayed feedback non-Markovian behavior neuronal firing statistics
2011/1/5
The instantaneous state of a neural network consists of both the degree of excitation of each neuron, the network is composed of, and positions of impulses in communication lines between neurons. In n...
The inverse problem of statistical mechanics involves finding the minimal Hamiltonian that is consistent with some observed set of correlation functions. This problem has received renewed interest in ...
Stable trimorphic coexistence in a lattice model of spatial competition with two site types
Stable trimorphic coexistence；lattice model
2011/1/5
I examine the effect of exogenous spatial heterogeneity on the coexistence of competing species using a simple model of non-hierarchical competition for site occupancy on a lattice. The sites on the l...
Two computational models to be used as tools for experimental research on the retinal implant are presented. In the first model, the electric field produced by a multi-electrode array in a uniform ret...
On the amino acid composition and mechanical stability of protein structures
the amino acid composition mechanical stability of protein structures
2011/1/5
Amino acid composition is an important determinant of protein structures. In this paper we investigate the relationship between amino acid composition and mechanical stability of protein sequences. We...
The term unfoldome has been recently used to indicate the universe of intrinsically disordered proteins. These proteins are characterized by an ensemble of high-flexible interchangeable conformations ...
A Unified Framework for Trees, Multi-Dimensional Scaling and Planar Graphs
Unified Framework for Trees Multi-Dimensional Scaling Planar Graphs
2011/1/5
Least squares trees, multi-dimensional scaling and Neighbor Nets are all different and popular ways of visualizing multi-dimensional data. The method of flexi-Weighted Least Squares (fWLS) is a powerf...
Speeding up evolutionary search by small fitness fluctuations
Speeding up evolutionary search fitness fluctuations
2011/1/5
We consider a fixed size population that undergoes an evolutionary adaptation in the weak mutuation rate limit, which we model as a biased Langevin process in the genotype space. We show analytically ...
Towards a theoretical understanding of false positives in DNA motif finding
theoretical understanding false positives DNA motif finding
2011/1/5
Detection of false-positive motifs is one of the main causes of low performance in motif finding methods. It is generally assumed that false-positives are mostly due to algorithmic weakness of motif-f...
This work faces the problem of the origin of the logarithmic character of the Gompertzian growth. We show that the macroscopic, deterministic Gompertz equation describes the evolution from the initial...
Dynamical quorum-sensing and synchronization of nonlinear oscillators coupled through an external medium
Dynamical quorum-sensing nonlinear oscillators coupled
2011/1/5
Many biological and physical systems exhibit population-density dependent transitions to synchronized oscillations in a process often termed "dynamical quorum sensing". Synchronization frequently aris...