Search results for "computational"
showing 10 items of 5884 documents
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 …
Efficient differentiation of embryonic stem cells into mesodermal precursors by BMP, retinoic acid and Notch signalling
2012
The ability to direct differentiation of mouse embryonic stem (ES) cells into specific lineages not only provides new insights into the pathways that regulate lineage selection but also has translational applications, for example in drug discovery. We set out to develop a method of differentiating ES cells into mesodermal cells at high efficiency without first having to induce embryoid body formation. ES cells were plated on a feeder layer of PA6 cells, which have membrane-associated stromal-derived inducing activity (SDIA), the molecular basis of which is currently unknown. Stimulation of ES/PA6 co-cultures with Bone Morphogenetic Protein 4 (BMP4) both favoured self-renewal of ES cells and…
Nonlocal Elastic-Damage Interface Mechanical Model
2007
The paper presents a nonlocal extension of the elastic-damage interface mechanical model, which is able to describe the effects of the spatially extended microstructure on the decohesion (or fracture) process along a surface. The key feature of the proposed model is an integral constitutive relation between tractions and displacement jumps at the interface. The presence of an integral kernel brings in the model an internal length measure, which characterizes the transition from the microscale, dominated by heterogeneities and discontinuous media, to the mesoscale, characterized as an enhanced homogenized continuum with nonlocal features. The motivations and the fields of applications of the…