Search results for "Quantitative Biology"
showing 10 items of 1025 documents
Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase
2015
Enzymes are the catalysts used by living organisms to accelerate chemical processes under physiological conditions. In this chapter, we illustrate the current view about the origin of their extraordinary rate enhancement based on molecular simulations and, in particular, on methods based on the combination of Quantum Mechanics and Molecular Mechanics potentials which provide a solution to treat the chemical reactivity of these large and complex molecular systems. Computational studies on Dihydrofolate Reductase have been selected as a conductor wire to present the evolution and difficulties to model chemical reactivity in enzymes. The results discussed here show that experimental observatio…
Distributions of oxygen, nutrient, and metabolic waste concentrations in multicellular spheroids and their dependence on spheroid parameters.
1991
The distribution of oxygen, nutrients and metabolic wastes in multicellular tumor spheroids and its dependence on the parameters characterizing the spheroid (i.e., spheroid geometry, diffusivity, and consumption/production rates of biological substances) have been investigated by a theoretical analysis: 1. Parameter dependence is qualitatively demonstrated and visualized. 2. Reduction of the number of variables by specific coordinate transformations made it possible to generate nomograms from which concentration distributions for any choice of parameter values may easily be obtained. In particular, these nomograms may also be used for estimating concentration profiles of metabolic waste pro…
Fluctuations and elastic properties of lipid membranes in the gel Lβ′ state: a coarse-grained Monte Carlo study
2010
We study the stress distribution profiles and the height and thickness fluctuations of lipid membranes in the gel L-beta ' state by Monte Carlo simulations of a generic coarse-grained model for lipid membranes, which reproduces many known properties of dipalmitoylphosphatidyncholine (DPPC) bilayers. The results are related to the corresponding properties of fluid membranes, and to theoretical predictions for crystalline and hexatic membranes. One striking observation is that the spontaneous curvature of the monolayers changes sign from the fluid to the gel phase. In the gel-phase, the long-wavelength height fluctuations are suppressed, and the fluctuation spectrum is highly anisotropic. In …
Rigid versus Flexible Protein Matrix: Light-Harvesting Complex II Exhibits a Temperature-Dependent Phonon Spectral Density
2018
Dynamics-function correlations are usually inferred when molecular mobility and protein function are simultaneously impaired at characteristic temperatures or hydration levels. In this sense, excitation energy transfer in the photosynthetic light-harvesting complex II (LHC II) is an untypical example because it remains fully functional even at cryogenic temperatures relying mainly on interactions of electronic states with protein vibrations. Here, we study the vibrational and conformational protein dynamics of monomeric and trimeric LHC II from spinach using inelastic neutron scattering (INS) in the temperature range of 20-305 K. INS spectra of trimeric LHC II reveal a distinct vibrational …
The Structure of Cholesterol in Lipid Rafts
2014
Rafts, or functional domains, are transient nano- or mesoscopic structures in the plasma membrane and are thought to be essential for many cellular processes such as signal transduction, adhesion, trafficking and lipid/protein sorting. Observations of these membrane heterogeneities have proven challenging, as they are thought to be both small and short-lived. With a combination of coarse-grained molecular dynamics simulations and neutron diffraction using deuterium labeled cholesterol molecules we observe raft-like structures and determine the ordering of the cholesterol molecules in binary cholesterol-containing lipid membranes. From coarse-grained computer simulations, heterogenous membra…
Importance sampling for Lambda-coalescents in the infinitely many sites model
2011
We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et. al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavar\'e (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et. al. (2008). We conclude with a performance comparison o…
Separation conditions on controlled Moran constructions
2017
It is well known that the open set condition and the positivity of the $t$-dimensional Hausdorff measure are equivalent on self-similar sets, where $t$ is the zero of the topological pressure. We prove an analogous result for a class of Moran constructions and we study different kinds of Moran constructions with this respect.
Active spike transmission in the neuron model with a winding threshold manifold
2012
International audience; We analyze spiking responses of excitable neuron model with a winding threshold manifold on a pulse stimulation. The model is stimulated with external pulse stimuli and can generate nonlinear integrate-and-fire and resonant responses typical for excitable neuronal cells (all-or-none). In addition we show that for certain parameter range there is a possibility to trigger a spiking sequence with a finite number of spikes (a spiking message) in the response on a short stimulus pulse. So active transformation of N incoming pulses to M (with M>N) outgoing spikes is possible. At the level of single neuron computations such property can provide an active "spike source" comp…
Flow properties and hydrodynamic interactions of rigid spherical microswimmers.
2017
We analyze a minimal model for a rigid spherical microswimmer and explore the consequences of its extended surface on the interplay between its self-propulsion and flow properties. The model is the first order representation of microswimmers, such as bacteria and algae, with rigid bodies and flexible propelling appendages. The flow field of such a microswimmer at finite distances significantly differs from that of a point-force (Stokeslet) dipole. For a suspension of microswimmers, we derive the grand mobility matrix that connects the motion of an individual swimmer to the active and passive forces and torques acting on all the swimmers. Our investigation of the mobility tensors reveals tha…
Dynamics of two competing species in the presence of Lévy noise sources
2010
We consider a Lotka-Volterra system of two competing species subject to multiplicative alpha-stable Lévy noise. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence both of a periodic driving term and an additive alpha-stable Lévy noise. We study the species dynamics, which is characterized by two different regimes, exclusion of one species and coexistence of both. We find quasi-periodic oscillations and stochastic resonance phenomenon in the dynamics of the competing species, analysing the role of the Lévy noise sources.