Search results for "Computation"
showing 10 items of 7362 documents
A Neurocomputational Approach to Trained and Transitive Relations in Equivalence Classes
2017
A stimulus class can be composed of perceptually different but functionally equivalent stimuli. The relations between the stimuli that are grouped in a class can be learned or derived from other stimulus relations. If stimulus A is equivalent to B, and B is equivalent to C, then the equivalence between A and C can be derived without explicit training. In this work we propose, with a neurocomputational model, a basic learning mechanism for the formation of equivalence. We also describe how the relatedness between the members of an equivalence class is developed for both trained and derived stimulus relations. Three classic studies on stimulus equivalence are simulated covering typical and at…
Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification
2008
The recently introduced non-stochastic and stochastic bond-based linear indices are been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. These improved modified descriptors are applied to several well-known data sets to validate each one of them. Particularly, Cramer's steroid data set has become a benchmark for the assessment of novel quantitative structure activity relationship methods. This data set has been used by several researchers using 3D-QSAR approaches such as Comparative Molecular Field Analysis, Molecular Quantum Similarity Measures, Comparative Molecular Moment Analysis, E-state, Mapping Prope…
A Fokker–Planck control framework for multidimensional stochastic processes
2013
AbstractAn efficient framework for the optimal control of probability density functions (PDFs) of multidimensional stochastic processes is presented. This framework is based on the Fokker–Planck equation that governs the time evolution of the PDF of stochastic processes and on tracking objectives of terminal configuration of the desired PDF. The corresponding optimization problems are formulated as a sequence of open-loop optimality systems in a receding-horizon control strategy. Many theoretical results concerning the forward and the optimal control problem are provided. In particular, it is shown that under appropriate assumptions the open-loop bilinear control function is unique. The res…
Solving fully randomized first-order linear control systems: Application to study the dynamics of a damped oscillator with parametric noise under sto…
2022
[EN] This paper is devoted to study random linear control systems where the initial condition, the final target, and the elements of matrices defining the coefficients are random variables, while the control is a stochastic process. The so-called Random Variable Transformation technique is adapted to obtain closed-form expressions of the probability density functions of the solution and of the control. The theoretical findings are applied to study the dynamics of a damped oscillator subject to parametric noise.
BROWNIAN DYNAMICS SIMULATIONS WITHOUT GAUSSIAN RANDOM NUMBERS
1991
We point out that in a Brownian dynamics simulation it is justified to use arbitrary distribution functions of random numbers if the moments exhibit the correct limiting behavior prescribed by the Fokker-Planck equation. Our argument is supported by a simple analytical consideration and some numerical examples: We simulate the Wiener process, the Ornstein-Uhlenbeck process and the diffusion in a Φ4 potential, using both Gaussian and uniform random numbers. In these examples, the rate of convergence of the mean first exit time is found to be nearly identical for both types of random numbers.
Physics of the nuclear pore complex: Theory, modeling and experiment
2021
Abstract The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular “nanomachine” known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the…
WENO schemes applied to the quasi-relativistic Vlasov-Maxwell model for laser-plasma interaction
2014
Abstract In this paper we focus on WENO-based methods for the simulation of the 1D Quasi-Relativistic Vlasov–Maxwell (QRVM) model used to describe how a laser wave interacts with and heats a plasma by penetrating into it. We propose several non-oscillatory methods based on either Runge–Kutta (explicit) or Time-Splitting (implicit) time discretizations. We then show preliminary numerical experiments.
ChIP-Seq from Limited Starting Material of K562 Cells and Drosophila Neuroblasts Using Tagmentation Assisted Fragmentation Approach
2019
Chromatin immunoprecipitation is extensively used to investigate the epigenetic profile and transcription factor binding sites in the genome. However, when the starting material is limited, the conventional ChIP-Seq approach cannot be implemented. This protocol describes a method that can be used to generate the chromatin profiles from as low as 100 human or 1,000 Drosophila cells. The method employs tagmentation to fragment the chromatin with concomitant addition of sequencing adaptors. The method generates datasets with high signal to noise ratio and can be subjected to standard tools for ChIP-Seq analysis.
Recent advances in surface plasmon resonance biosensors for microRNAs detection
2020
miRNAs are a large family of non-coding RNAs which play important roles in translational and post-transcriptional regulation of gene expression and biological processes. Abnormal expression of miRNAs is related to the initiation and progression of different diseases which make them be promising candidates for early medical diagnostics. Thus, accurate detection of miRNAs has great significance for disorder diagnosis. Nevertheless, their intrinsic characteristics such as short sequence, low concentration and sequence homology challenge routine techniques. The detection assays need to be extremely sensitive and selective in small value of intricate RNA samples. Biosensor-based strategies have …
Multicellular tumor spheroids: an underestimated tool is catching up again.
2009
The present article highlights the rationale, potential and flexibility of tumor spheroid mono- and cocultures for implementation into state of the art anti-cancer therapy test platforms. Unlike classical monolayer-based models, spheroids strikingly mirror the 3D cellular context and therapeutically relevant pathophysiological gradients of in vivo tumors. Some concepts for standardization and automation of spheroid culturing, monitoring and analysis are discussed, and the challenges to define the most convenient analytical endpoints for therapy testing are outlined. The potential of spheroids to contribute to either the elimination of poor drug candidates at the pre-animal and pre-clinical …