154 research outputs found
Kinetic hierarchy and propagation of chaos in biological swarm models
We consider two models of biological swarm behavior. In these models, pairs
of particles interact to adjust their velocities one to each other. In the
first process, called 'BDG', they join their average velocity up to some noise.
In the second process, called 'CL', one of the two particles tries to join the
other one's velocity. This paper establishes the master equations and BBGKY
hierarchies of these two processes. It investigates the infinite particle limit
of the hierarchies at large time-scale. It shows that the resulting kinetic
hierarchy for the CL process does not satisfy propagation of chaos. Numerical
simulations indicate that the BDG process has similar behavior to the CL
process
Fast porous visco-hyperelastic soft tissue model for surgery simulation: Application to liver surgery
International audienceUnderstanding and modeling liver biomechanics represents a significant challenge due to its complex nature. In this paper, we tackle this issue in the context of real time surgery simulation where a compromise between biomechanical accuracy and computational efficiency must be found. We describe a realistic liver model including hyperelasticity, porosity and viscosity that is implemented within an implicit time integration scheme. To optimize its computation, we introduce the Multiplicative Jacobian Energy Decomposition (MJED) method for discretizing hyperelastic materials on linear tetrahedral meshes which leads to faster matrix assembly than the standard Finite Element Method. Viscohyperelasticity is modeled by Prony series while the mechanical eff ect of liver perfusion is represented with a linear Darcy law. Dynamic mechanical analysis has been performed on 60 porcine liver samples in order to identify some visco-elastic parameters. Finally, we show that liver deformation can be simulated in real-time on a coarse mesh and study the relative eff ects of the hyperelastic, viscous and porous components on the liver biomechanics
Temperature dependence of ESR intensity for the nanoscale molecular magnet V15
The electron spin resonance (ESR) of nanoscale molecular magnet is studied. Since the Hamiltonian of has a large
Hilbert space and numerical calculations of the ESR signal evaluating the Kubo
formula with exact diagonalization method is difficult, we implement the
formula with the help of the random vector technique and the Chebyshev
polynominal expansion, which we name the double Chebyshev expansion method. We
calculate the temperature dependence of the ESR intensity of and
compare it with the data obtained in experiment. As another complementary
approach, we also implement the Kubo formula with the subspace iteration method
taking only important low-lying states into account. We study the ESR
absorption curve below by means of both methods. We find that side
peaks appear due to the Dzyaloshinsky-Moriya interaction and these peaks grows
as temperature decreases.Comment: 9 pages, 4 figures. To appear in J. Phys. Soc. Jpn. Supp
Efficient Recursion Method for Inverting Overlap Matrix
A new O(N) algorithm based on a recursion method, in which the computational
effort is proportional to the number of atoms N, is presented for calculating
the inverse of an overlap matrix which is needed in electronic structure
calculations with the the non-orthogonal localized basis set. This efficient
inverting method can be incorporated in several O(N) methods for
diagonalization of a generalized secular equation. By studying convergence
properties of the 1-norm of an error matrix for diamond and fcc Al, this method
is compared to three other O(N) methods (the divide method, Taylor expansion
method, and Hotelling's method) with regard to computational accuracy and
efficiency within the density functional theory. The test calculations show
that the new method is about one-hundred times faster than the divide method in
computational time to achieve the same convergence for both diamond and fcc Al,
while the Taylor expansion method and Hotelling's method suffer from numerical
instabilities in most cases.Comment: 17 pages and 4 figure
Computing the lower and upper bounds of Laplace eigenvalue problem: by combining conforming and nonconforming finite element methods
This article is devoted to computing the lower and upper bounds of the
Laplace eigenvalue problem. By using the special nonconforming finite elements,
i.e., enriched Crouzeix-Raviart element and extension , we get
the lower bound of the eigenvalue. Additionally, we also use conforming finite
elements to do the postprocessing to get the upper bound of the eigenvalue. The
postprocessing method need only to solve the corresponding source problems and
a small eigenvalue problem if higher order postprocessing method is
implemented. Thus, we can obtain the lower and upper bounds of the eigenvalues
simultaneously by solving eigenvalue problem only once. Some numerical results
are also presented to validate our theoretical analysis.Comment: 19 pages, 4 figure
Asymptotic Expansions for Stationary Distributions of Perturbed Semi-Markov Processes
New algorithms for computing of asymptotic expansions for stationary
distributions of nonlinearly perturbed semi-Markov processes are presented. The
algorithms are based on special techniques of sequential phase space reduction,
which can be applied to processes with asymptotically coupled and uncoupled
finite phase spaces.Comment: 83 page
Sequence Defined Disulfide-Linked Shuttle for Strongly Enhanced Intracellular Protein Delivery
Intracellular protein transduction technology is opening the door for a promising alternative to gene therapy. Techniques have to address all critical steps, like efficient cell uptake, endolysosomal escape, low toxicity, while maintaining full functional activity of the delivered protein. Here, we present the use of a chemically precise, structure defined three-arm cationic oligomer carrier molecule for protein delivery. This carrier of exact and low molecular weight combines good cellular uptake with efficient endosomal escape and low toxicity. The protein cargo is covalently attached by a bioreversible disulfide linkage. Murine 3T3 fibroblasts could be transduced very efficiently with cargo nlsEGFP, which was tagged with a nuclear localization signal. We could show subcellular delivery of the nlsEGFP to the nucleus, confirming cytosolic delivery and expected subsequent subcellular trafficking. Transfection efficiency was concentration-dependent in a directly linear mode and 20-fold higher in comparison with HIV-TAT-nlsEGFP containing a functional TAT transduction domain. Furthermore, β-galactosidase as a model enzyme cargo, modified with the carrier oligomer, was transduced into neuroblastoma cells in enzymatically active form
Cognition based bTBI mechanistic criteria; a tool for preventive and therapeutic innovations
Blast-induced traumatic brain injury has been associated with neurodegenerative and neuropsychiatric disorders. To date, although damage due to oxidative stress appears to be important, the specific mechanistic causes of such disorders remain elusive. Here, to determine the mechanical variables governing the tissue damage eventually cascading into cognitive deficits, we performed a study on the mechanics of rat brain under blast conditions. To this end, experiments were carried out to analyse and correlate post-injury oxidative stress distribution with cognitive deficits on a live rat exposed to blast. A computational model of the rat head was developed from imaging data and validated against in vivo brain displacement measurements. The blast event was reconstructed in silico to provide mechanistic thresholds that best correlate with cognitive damage at the regional neuronal tissue level, irrespectively of the shape or size of the brain tissue types. This approach was leveraged on a human head model where the prediction of cognitive deficits was shown to correlate with literature findings. The mechanistic insights from this work were finally used to propose a novel helmet design roadmap and potential avenues for therapeutic innovations against blast traumatic brain injury
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