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At least 271 records · Page 15Linked to original sources
PubMed2004

The FLUKA code for space applications: recent developments.

The FLUKA Monte Carlo transport code is widely used for fundamental research, radioprotection and dosimetry, hybrid nuclear energy system and cosmic ray calculations. The validity of its physical models has been benchmarked against a variety of experimental data over a wide range of energies, ranging from accelerator data to cosmic ray showers in the earth atmosphere. The code is presently undergoing several developments in order to better fit the needs of space applications. The generation of particle spectra according to up-to-date cosmic ray data as well as the effect of the solar and geomagnetic modulation have been implemented and already successfully applied to a variety of problems. The implementation of suitable models for heavy ion nuclear interactions has reached an operational stage. At medium/high energy FLUKA is using the DPMJET model. The major task of incorporating heavy ion interactions from a few GeV/n down to the threshold for inelastic collisions is also progressing and promising results have been obtained using a modified version of the RQMD-2.4 code. This interim solution is now fully operational, while waiting for the development of new models based on the FLUKA hadron-nucleus interaction code, a newly developed QMD code, and the implementation of the Boltzmann master equation theory for low energy ion interactions.

Computer Simulation↗
PubMed2006

Mutation model for nucleotide sequences based on crystal basis.

A nucleotide sequence is identified, using a two (four)-letter alphabet, by the the labels of a vector state of an irreducible representation of Uq-->0(sl(2)) (Uq-->0(sl(2) plus sign in circle sl(2))). A master equation for the distribution function is written, where the intensity of the one-spin flip is assumed to depend on the variation of the labels of the state. In the two-letter approximation, the numerically computed equilibrium distribution for short sequences is fitted nicely by a Yule distribution, which is the observed distribution of the ranked short oligonucleotides frequency in DNA. The four-letter alphabet description, applied to the codons, is able to reproduce the form of the fitted rank-ordered usage frequencies distribution.

Base Sequence↗
PubMed2004

Binding energies of water to lithiated valine: formation of solution-phase structure in vacuo.

Dissociation kinetics for loss of a water molecule from hydrated ions of lithiated valine, alanine ethyl ester and betaine are determined using blackbody infrared radiative dissociation at temperatures between -60 and 110 degrees C. From master equation modeling of these data, values of the threshold dissociation energy are obtained for clusters containing one through three water molecules. By comparing the values for valine with its two isomers, one a model for the nonzwitterion structure, the other a model for the zwitterion structure, information about the structure of valine in these hydrated clusters is inferred. Structures, relative energies, and water binding energies for these ions are also calculated at the B3LYP/6-31++G** level of theory. With one water molecule, both experiment and theory indicate that valine is not a zwitterion and that the lithium ion coordinates with the amino nitrogen and the carbonyl oxygen (NO coordinated) and the water molecule interacts directly with the lithium ion. With two water molecules, the zwitterion and nonzwitterion structures are nearly isoenergetic, but the experiment clearly indicates a NO-coordinated nonzwitterion structure. With three water molecules, both the experimental data and theory indicate that the lithium ion binds to the carboxylate group of valine, i.e., valine is zwitterionic with three water molecules. The agreement between the experimentally determined and calculated binding energies is good for all the clusters, with deviations of <== 0.12 eV.

Alanine↗
PubMed2006

A Davies/Hahn multi-sequence for studies of spin relaxation in pulsed ENDOR.

We extend earlier studies of the effects of relaxation on the intensities of pulsed ENDOR signals by introducing a Davies/Hahn (D/H) pulsed ENDOR multi-sequence that corresponds to a series of Davies sequences with the preparation pulse 'turned off'. In this pulse train, the Hahn [pi/2, pi] detection pulse pair of sequence n-1 both generates the echo detected for that sequence and acts as the preparation portion of sequence n, in effect replacing the pi preparation pulse of the Davies sequence. We show both theoretically, through a master-equation approach, and with both (1)H(I=1/2) and (14)N(I=1) ENDOR experiments on the non-heme Fe enzymes, superoxide reductase (SOR) (S=1/2) and AntDO (S=3/2), that under conditions of high electron-spin polarization (high microwave frequency/low temperature) the D/H multi-sequence allows simplification of ENDOR spectra by suppression of nuclear transitions associated with the m(S)=+1/2 (alpha) manifold. As such suppression depends on the sign of A, it allows determination of this sign. The suppression as a function of the time between individual sequences is found to exhibit behaviors that can be classified into three regimes of the ratio of cross-relaxation to spin-lattice relaxation rates: strong cross-relaxation (X-case); comparable rates (XL); negligible cross relaxation (L). Interestingly, the ENDOR behavior of the S=1/2 SOR center indicates it is an L case, while the S=3/2 AntDO is an L case. Overall, the D/H protocol appears to be a robust and general tool for using relaxation effects to manipulate ENDOR spectra.

Electron Spin Resonance Spectroscopy↗
PubMed2004

Multivariate analysis of noise in genetic regulatory networks.

Stochasticity is an intrinsic property of genetic regulatory networks due to the low copy numbers of the major molecular species, such as, DNA, mRNA, and regulatory proteins. Therefore, investigation of the mechanisms that reduce the stochastic noise is essential in understanding the reproducible behaviors of real organisms and is also a key to design synthetic genetic regulatory networks that can reliably work. We use an analytical and systematic method, the linear noise approximation of the chemical master equation along with the decoupling of a stoichiometric matrix. In the analysis of fluctuations of multiple molecular species, the covariance is an important measure of noise. However, usually the representation of a covariance matrix in the natural coordinate system, i.e. the copy numbers of the molecular species, is intractably complicated because reactions change copy numbers of more than one molecular species simultaneously. Decoupling of a stoichiometric matrix, which is a transformation of variables, significantly simplifies the representation of a covariance matrix and elucidates the mechanisms behind the observed fluctuations in the copy numbers. We apply our method to three types of fundamental genetic regulatory networks, that is, a single-gene autoregulatory network, a two-gene autoregulatory network, and a mutually repressive network. We have found that there are multiple noise components differently originating. Each noise component produces fluctuation in the characteristic direction. The resulting fluctuations in the copy numbers of the molecular species are the sum of these fluctuations. In the examples, the limitation of the negative feedback in noise reduction and the trade-off of fluctuations in multiple molecular species are clearly explained. The analytical representations show the full parameter dependence. Additionally, the validity of our method is tested by stochastic simulations.

Animals↗
PubMed2004

Analytic solution of Hubbell's model of local community dynamics.

Recent theoretical approaches to community structure and dynamics reveal that many large-scale features of community structure (such as species-rank distributions and species-area relations) can be explained by a so-called neutral model. Using this approach, species are taken to be equivalent and trophic relations are not taken into account explicitly. Here we provide a general analytic solution to the local community model of Hubbell's neutral theory of biodiversity by recasting it as an urn model, i.e. a Markovian description of states and their transitions. Both stationary and time-dependent distributions are analysed. The stationary distribution-also called the zero-sum multinomial-is given in closed form. An approximate form for the time-dependence is obtained by using an expansion of the master equation. The temporal evolution of the approximate distribution is shown to be a good representation for the true temporal evolution for a large range of parameter values.

Biodiversity↗
PubMed2000

Energy transfer among CP29 chlorophylls: calculated Förster rates and experimental transient absorption at room temperature.

The energy transfer rates between chlorophylls in the light harvesting complex CP29 of higher plants at room temperature were calculated ab initio according to the Förster mechanism (Förster T. 1948, Ann. Physik. 2:55-67). Recently, the transition moment orientation of CP29 chlorophylls was determined by differential linear dichroism and absorption spectroscopy of wild-type versus mutant proteins in which single chromophores were missing (Simonetto R., Crimi M., Sandonà D., Croce R., Cinque G., Breton J., and Bassi R. 1999. Biochemistry. 38:12974-12983). In this way the Q(y) transition energy and chlorophyll a/b affinity of each binding site was obtained and their characteristics supported by reconstruction of steady-state linear dichroism and absorption spectra at room temperature. In this study, the spectral form of individual chlorophyll a and b ligands within the protein environment was experimentally determined, and their extinction coefficients were also used to evaluate the absolute overlap integral between donors and acceptors employing the Stepanov relation for both the emission spectrum and the Stokes shift. This information was used to calculate the time-dependent excitation redistribution among CP29 chlorophylls on solving numerically the Pauli master equation of the complex: transient absorption measurements in the (sub)picosecond time scale were simulated and compared to pump-and-probe experimental data in the Q(y) region on the native CP29 at room temperature upon selective excitation of chlorophylls b at 640 or 650 nm. The kinetic model indicates a bidirectional excitation transfer over all CP29 chlorophylls a species, which is particularly rapid between the pure sites A1-A2 and A4-A5. Chlorophylls b in mixed sites act mostly as energy donors for chlorophylls a, whereas site B5 shows high and bidirectional coupling independent of the pigment hosted.

Biophysical Phenomena↗
PubMed2001

Stochastic simulation of hemagglutinin-mediated fusion pore formation.

Studies on fusion between cell pairs have provided evidence that opening and subsequent dilation of a fusion pore are stochastic events. Therefore, adequate modeling of fusion pore formation requires a stochastic approach. Here we present stochastic simulations of hemagglutinin (HA)-mediated fusion pore formation between HA-expressing cells and erythrocytes based on numerical solutions of a master equation. The following elementary processes are taken into account: 1) lateral diffusion of HA-trimers and receptors, 2) aggregation of HA-trimers to immobilized clusters, 3) reversible formation of HA-receptor contacts, and 4) irreversible conversion of HA-receptor contacts into stable links between HA and the target membrane. The contact sites between fusing cells are modeled as superimposed square lattices. The model simulates well the statistical distribution of time delays measured for the various intermediates of fusion pore formation between cell-cell fusion complexes. In particular, these are the formation of small ion-permissive and subsequent lipid-permissive fusion pores detected experimentally (R. Blumenthal, D. P. Sarkar, S. Durell, D. E. Howard, and S. J., J. Cell Biol. 135:63-71). Moreover, by averaging the simulated individual stochastic time courses across a larger population of cell-cell-complexes the model also provides a reasonable description of kinetic measurements on lipid mixing in cell suspensions (T. Danieli, S. L. Pelletier, Y.I. Henis, and J. M. White, 1996, J. Cell Biol. 133:559-569).

Cell Fusion↗
PubMed2003

Near-critical phenomena in intracellular metabolite pools.

The supply and consumption of metabolites in living cells are catalyzed by enzymes. Here we consider two of the simplest schemes where one substrate is eliminated through Michaelis-Menten kinetics, and where two types of substrates are joined together by an enzyme. It is demonstrated how steady-state substrate concentrations can change ultrasensitively in response to changes in their supply rates and how this is coupled to slow relaxation back to steady state after a perturbation. In the one-substrate system, such near-critical behavior occurs when the supply rate approaches the maximal elimination rate, and in the two-substrate system it occurs when the rates of substrate supply are almost balanced. As systems that operate near criticality tend to display large random fluctuations, we also carried out a stochastic analysis using analytical approximations of master equations and compared the results with molecular-level Monte Carlo simulations. It was found that the significance of random fluctuations was directly coupled to the steady-state sensitivity and that the two substrates can fluctuate greatly because they are anticorrelated in such a way that the product formation rate displays only small variation. Basic relations are highlighted and biological implications are discussed.

Biochemical Phenomena↗
PubMed1983

Kinetic model for the interaction of myosin subfragment 1 with regulated actin.

A one-dimensional kinetic Ising model is developed to describe the binding of myosin subfragment 1 (SF-1) to regulated actin. The model allows for cooperative interactions between individual actin sites with bound SF-1 ligands rather than assuming that groups of actin monomer sites change their state in a cooperative fashion. With the triplet closure approximation, the model yields a set of 16 independent differential (master) equations which may be solved numerically to yield the extent of binding as a function of time. The predictions of the model are compared with experiments on the transient binding of SF-1 to regulated actin in the presence of Ca2+ and in the absence of Ca2+ with varying amounts of SF-1 prebound to the actin filament and on the equilibrium binding of SF-1 X ADP to regulated actin in the absence of Ca2+. In all cases, the calculations fit the data to within the experimental errors. In the case of SF-1 X ADP, the results suggest that a repulsive interaction exists between adjacently bound SF-1 at the ends of two neighboring seven-site actin units.

Actins↗
PubMed1993

Theory of photoselection by intense light pulses. Influence of reorientational dynamics and chemical kinetics on absorbance measurements.

The theory of absorbance measurements on a system (e.g., chromophore(s) in a protein) that undergoes a sequence of reactions initiated by a linearly polarized light pulse is developed for excitation pulses of arbitrary intensity. This formalism is based on a set of master equations describing the time evolution of the orientational distribution function of the various species resulting from excitation, reorientational dynamics, and chemical kinetics. For intense but short excitation pulses, the changes in absorbance (for arbitrary polarization directions of the excitation and probe pulses) and the absorption anisotropy are expressed in terms of reorientational correlation functions. The influence of the internal motions of the chromophore as well as the overall motions of the molecules is considered. When the duration of the excitation pulse is long compared to the time-scale of internal motions but comparable to the overall correlation time of the molecule that is reorienting isotropically, the problem of calculating the changes in absorbance is reduced to the solution of a set of first-order coupled differential equations. Emphasis is placed on obtaining explicit results for quantities that are measured in photolysis and fluorescence experiments so as to facilitate the analysis of experimental data.

Binding Sites↗
PubMed1994

Energy transfer in the inhomogeneously broadened core antenna of purple bacteria: a simultaneous fit of low-intensity picosecond absorption and fluorescence kinetics.

The excited state decay kinetics of chromatophores of the purple photosynthetic bacterium Rhodospirillum rubrum have been recorded at 77 K using picosecond absorption difference spectroscopy under strict annihilation free conditions. The kinetics are shown to be strongly detection wavelength dependent. A simultaneous kinetic modeling of these experiments together with earlier fluorescence kinetics by numerical integration of the appropriate master equation is performed. This model, which accounts for the spectral inhomogeneity of the core light-harvesting antenna of photosynthetic purple bacteria, reveals three qualitatively distinct stages of excitation transfer with different time scales. At first a fast transfer to a local energy minimum takes place (approximately 1 ps). This is followed by a much slower transfer between different energy minima (10-30 ps). The third component corresponds to the excitation transfer to the reaction center, which depends on its state (60 and 200 ps for open and closed, respectively) and seems also to be the bottleneck in the overall trapping time. An acceptable correspondence between theoretical and experimental decay kinetics is achieved at 77 K and at room temperature by assuming that the width of the inhomogeneous broadening is 10-15 nm and the mean residence time of the excitation in the antenna lattice site is 2-3 ps.

Bacterial Chromatophores↗
PubMed1994

Kinetic modeling of exciton migration in photosynthetic systems. 2. Simulations of excitation dynamics in two-dimensional photosystem I core antenna/reaction center complexes.

Kinetic modeling of the exciton migration in the cyanobacterial photosystem I core complex from Synechococcus sp. was performed by an exact solution of the Pauli master equation for exciton motion. A square two-dimensional 10 x 10 pigment lattice and a Förster dipole-dipole coupling between chromophores was assumed. We calculated decay-associated spectra and lifetimes and compared them to the corresponding experimental data from picosecond fluorescence and transient absorption obtained by global analysis. Seven spectral chlorophyll(Chl) forms, identical in shape but shifted in their absorption maximums, were used to describe the non-homogeneous broadening of the PS I-100 particle absorption spectrum. The optimized Chl lattice arrangement best reproducing the experimental decay-associated spectra as well as the steady-state fluorescence spectrum indicated the long-wavelength-absorbing Chls forming a cluster in the corner of the lattice with the reaction center (RC) placed apart at a distance of two lattice constants. The variable parameters, i.e., the charge separation rate in the RC and the lattice constant a, were found to be optimal at kRC = 2.3 ps-1 and a = 1.14 nm, respectively. The surprising conclusions of the simulations is that Chls with absorption maxima as long a 724 nm have to be taken into account to describe the time-resolved spectra of this PS I particle properly. The dependencies of the exciton decay in the model PS I particle on the excitation wavelength and on the temperature are discussed. We also show that the excited state decay of similar PS I particles that lack the long-wavelength absorbing Chls is nearly mono-exponential. Various critical factors that limit the general reliability of the conclusions of such simulations are discussed in detail.

Biophysical Phenomena↗
PubMed1995

Energy transfer in spectrally inhomogeneous light-harvesting pigment-protein complexes of purple bacteria.

Energy transfer within the peripheral light-harvesting antenna of the purple bacteria Rhodobacter sphaeroides and Rhodopseudomonas palustris was studied by one- and two-color pump-probe absorption spectroscopy with approximately 100-fs tunable pulses at room temperature and at 77 K. The energy transfer from B800 to B850 occurs with a time constant of 0.7 +/- 0.05 ps at room temperature and 1.8 +/- 0.2 ps at 77 K and is similar in both species. Anisotropy measurements suggest a limited but fast B800 <--> B800 transfer time (tau approximately 0.3 ps). This is analyzed as incoherent hopping of the excitation in a system of spectrally inhomogeneous antenna pigment-protein complexes, by a master equation approach. The simulations show that the measured B800 dynamics is well described as energy transfer with a characteristic average nearest-neighbor pairwise transfer time of 0.35 ps among approximately 10 Bchl molecules in a circular arrangement, in good agreement with the recent high-resolution structure of LH2. The possible presence of fast intramolecular relaxation processes within the Bchl a molecule was investigated by measurement of time-resolved difference absorption spectra and kinetics of Bchl a in solution and in low-temperature glasses. From these measurements it is concluded that fast transients observed at room temperature are due mainly to solvation processes, whereas at 77 K predominantly slower (> 10-ps) relaxation occurs.

Bacterial Chromatophores↗
PubMed1996

Stochastic simulation of the transducin GTPase cycle.

On rod disc membranes, single photoactivated rhodopsin (R*) molecules catalytically activate many copies of the G-protein (Gt), which in turn binds and activates the effector (phosphodiesterase). We have performed master equation simulations of the underlying diffusional protein interactions on a rectangular 1-micron2 model membrane, divided into 15 x 15 cells. Mono- and bimolecular reactions occur within cells, and diffusional transitions occur between (neighboring) cells. Reaction and diffusion constants yield the related probabilities for the stochastic transitions. The calculated kinetics of active effector form a response that is essentially determined by the stochastic lifetime distribution of R* (with characteristic time tau R*) and the reaction constants of Gt activation. Only a short tau R* (approximately 0.3 s) and a high catalytic rate (3000-4000 Gt s-1 R*-1) are consistent with electrophysiological data. Although R* shut-off limits the rise of the response, the lifetime distribution of free R* is not translated into a corresponding variability of the response peaks, because 1) the lifetime distribution of catalytically engaged R* is distorted, 2) small responses are enlarged by an overshoot of active effector, and 3) larger responses tend to undergo saturation. Comparison of these results to published photocurrent waveforms may open ways to understand the relative uniformity of the rod response.

Animals↗
PubMed1999

Probabilistic modeling of shear-induced formation and breakage of doublets cross-linked by receptor-ligand bonds.

A model was constructed to describe previously published experiments of shear-induced formation and breakage of doublets of red cells and of latexes cross-linked by receptor-ligand bonds (. Biophys. J. 65:1318-1334; Tees and Goldsmith. 1996. Biophys. J. 71:1102-1114;. Biophys. J. 71:1115-1122). The model, based on McQuarrie's master equations (1963. J. Phys. Chem. 38:433-436), provides unifying treatments for three distinctive time periods in the experiments of particles in a Couette flow in which a doublet undergoes 1) formation upon two-body collision between singlets; 2) evolution of bonds at low shear rate; and 3) break-up at high shear rate. Neglecting the applied force at low shear rate, the probability of forming a doublet per collision as well as the evolution of probability distribution of bonds in a preformed doublet were solved analytically and found to be in quite good agreement with measurements. At high shear rate with significant force acting to accelerate bond dissociation, the predictions for break-up of doublets were obtained numerically and compared well with data in both individual and population studies. These comparisons enabled bond kinetic parameters for three types of particles cross-linked by two receptor-ligand systems to be calculated, which agreed well with those computed from Monte Carlo simulations. This work can be extended to analyze kinetics of receptor-ligand binding in cell aggregates, such as those of neutrophils and platelets in the circulation.

Cell Aggregation↗
PubMed2002

Application of the diffusion-collision model to the folding of three-helix bundle proteins.

The diffusion-collision model has been successful in explaining many features of protein folding kinetics, particularly for helical proteins. In the model the folding reaction is described in terms of coupled chemical kinetic (Master) equations of coarse grained entities, called microdomains. Here, the diffusion-collision model is applied to compute the folding kinetics of four three-helix bundle proteins, all of which fold on a time scale of tens of microseconds and appear to have two-state folding. The native structure and the stability of the helical microdomains are used to determine the parameters of the model. The formulation allows computation of the overall rate and determination of the importance of kinetic intermediates. The proteins considered are the B domain of protein A (1BDC), the Engrailed Homeodomain (1ENH), the peripheral sub-unit-binding domain (1EBD C-chain) and the villin headpiece subdomain (1VII). The results for the folding time of protein A, the Engrailed Homeodomain, and 1EBD C-chain are in agreement with experiment, while 1VII is not stable in the present model. In the three proteins that are stable, two-state folding is predicted by the diffusion-collision model. This disagrees with published assertions that multistate kinetics would be obtained from the model. The contact order prediction agrees with experiment for protein A, but yields values that are a factor of 40, 30 and 15 too slow for 1ENH, 1EBD C-chain and 1VII. The effect of mutants on folding is described for protein A and it is demonstrated that significant intermediate concentrations (i.e. deviation from two-state folding) can occur if the stability of some of the helical microdomains is increased. A linear relationship between folding time and the length of the loop between helices B and C in protein A is demonstrated; this is not evident in the contact order description.

Amino Acid Sequence↗
PubMed2002

Simple physical models connect theory and experiment in protein folding kinetics.

Our understanding of the principles underlying the protein-folding problem can be tested by developing and characterizing simple models that make predictions which can be compared to experimental data. Here we extend our earlier model of folding free energy landscapes, in which each residue is considered to be either folded as in the native state or completely disordered, by investigating the role of additional factors representing hydrogen bonding and backbone torsion strain, and by using a hybrid between the master equation approach and the simple transition state theory to evaluate kinetics near the free energy barrier in greater detail. Model calculations of folding phi-values are compared to experimental data for 19 proteins, and for more than half of these, experimental data are reproduced with correlation coefficients between r=0.41 and 0.88; calculations of transition state free energy barriers correlate with rates measured for 37 single domain proteins (r=0.69). The model provides insight into the contribution of alternative-folding pathways, the validity of quasi-equilibrium treatments of the folding landscape, and the magnitude of the Arrhenius prefactor for protein folding. Finally, we discuss the limitations of simple native-state-based models, and as a more general test of such models, provide predictions of folding rates and mechanisms for a comprehensive set of over 400 small protein domains of known structure.

Bacterial Proteins↗