146,704 research outputs found
Quasisolitons in self-diffusive excitable systems, or Why asymmetric diffusivity does not violate the Second Law
Solitons, defined as nonlinear waves which can reflect from boundaries or
transmit through each other, are found in conservative, fully integrable
systems. Similar phenomena, dubbed quasi-solitons, have been observed also in
dissipative, "excitable" systems, either at finely tuned parameters (near a
bifurcation) or in systems with cross-diffusion. Here we demonstrate that
quasi-solitons can be robustly observed in excitable systems with excitable
kinetics and with self-diffusion only. This includes quasi-solitons of fixed
shape (like KdV solitons) or envelope quasi-solitons (like NLS solitons). This
can happen in systems with more than two components, and can be explained by
effective cross-diffusion, which emerges via adiabatic elimination of a fast
but diffusing component. We describe here a reduction procedure can be used for
the search of complicated wave regimes in multi-component, stiff systems by
studying simplified, soft systems.Comment: 11 pages, 2 figures, as accepted to Scientific Reports on 2016/07/0
Interplay of water and a supramolecular capsule for catalysis of reductive elimination reaction from gold.
Supramolecular assemblies have gained tremendous attention due to their ability to catalyze reactions with the efficiencies of natural enzymes. Using ab initio molecular dynamics, we identify the origin of the catalysis by the supramolecular capsule Ga4L612- on the reductive elimination reaction from gold complexes and assess their similarity to natural enzymes. By comparing the free energies of the reactants and transition states for the catalyzed and uncatalyzed reactions, we determine that an encapsulated water molecule generates electric fields that contributes the most to the reduction in the activation free energy. Although this is unlike the biomimetic scenario of catalysis through direct host-guest interactions, the electric fields from the nanocage also supports the transition state to complete the reductive elimination reaction with greater catalytic efficiency. However it is also shown that the nanocage poorly organizes the interfacial water, which in turn creates electric fields that misalign with the breaking bonds of the substrate, thus identifying new opportunities for catalytic design improvements in nanocage assemblies
Impact of rapeseed press-cake on Maillard reaction in a cookie model system
Rapeseed press-cake (RPC) is a byproduct of rapeseed oil production, rich in proteins and fiber. The aim of this study was to investigate the impact of cold pressed RPC, RPC fiber isolate and RPC alkaline extract on the formation of acrylamide and 5-hydroxymethylfufural (HMF) in cookies. Both compounds were influenced by the ingredients: the addition of RPC led to a significant dose-dependent increase of HMF in the cookies and to an increase of acrylamide up to 66.9%. On the contrary, acrylamide concentration was reduced down to 39.6% in presence of the alkaline extract and down to 4.4% in the presence of the fiber extract. The Michael addition of free amino acids to acrylamide was further investigated by high-resolution mass spectrometry (HRMS) revealing that cysteine was the preferred nucleophile for acrylamide elimination
Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models
We use the Litvinov-Maslov correspondence principle to reduce and hybridize
networks of biochemical reactions. We apply this method to a cell cycle
oscillator model. The reduced and hybridized model can be used as a hybrid
model for the cell cycle. We also propose a practical recipe for detecting
quasi-equilibrium QE reactions and quasi-steady state QSS species in
biochemical models with rational rate functions and use this recipe for model
reduction. Interestingly, the QE/QSS invariant manifold of the smooth model and
the reduced dynamics along this manifold can be put into correspondence to the
tropical variety of the hybridization and to sliding modes along this variety,
respectivelyComment: conference SASB 2011, to be published in Electronic Notes in
Theoretical Computer Scienc
Rigorous elimination of fast stochastic variables from the linear noise approximation using projection operators
The linear noise approximation (LNA) offers a simple means by which one can
study intrinsic noise in monostable biochemical networks. Using simple physical
arguments, we have recently introduced the slow-scale LNA (ssLNA) which is a
reduced version of the LNA under conditions of timescale separation. In this
paper, we present the first rigorous derivation of the ssLNA using the
projection operator technique and show that the ssLNA follows uniquely from the
standard LNA under the same conditions of timescale separation as those
required for the deterministic quasi-steady state approximation. We also show
that the large molecule number limit of several common stochastic model
reduction techniques under timescale separation conditions constitutes a
special case of the ssLNA.Comment: 10 pages, 1 figure, submitted to Physical Review E; see also BMC
Systems Biology 6, 39 (2012
Self-immolative linkers in polymeric delivery systems
There has been significant interest in the methodologies of controlled release for a diverse range of applications spanning drug delivery, biological and chemical sensors, and diagnostics. The advancement in novel substrate-polymer coupling moieties has led to the discovery of self-immolative linkers. This new class of linker has gained popularity in recent years in polymeric release technology as a result of stable bond formation between protecting and leaving groups, which becomes labile upon activation, leading to the rapid disassembly of the parent polymer. This ability has prompted numerous studies into the design and development of self-immolative linkers and the kinetics surrounding their disassembly. This review details the main concepts that underpin self-immolative linker technologies that feature in polymeric or dendritic conjugate systems and outlines the chemistries of amplified self-immolative elimination
Model reduction of biochemical reactions networks by tropical analysis methods
We discuss a method of approximate model reduction for networks of
biochemical reactions. This method can be applied to networks with polynomial
or rational reaction rates and whose parameters are given by their orders of
magnitude. In order to obtain reduced models we solve the problem of tropical
equilibration that is a system of equations in max-plus algebra. In the case of
networks with nonlinear fast cycles we have to solve the problem of tropical
equilibration at least twice, once for the initial system and a second time for
an extended system obtained by adding to the initial system the differential
equations satisfied by the conservation laws of the fast subsystem. The two
steps can be reiterated until the fast subsystem has no conservation laws
different from the ones of the full model. Our method can be used for formal
model reduction in computational systems biology
- …