Coarse-grained model of entropic allostery

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand changes the intramolecular vibrational entropy, not just the mean static structure. We present a quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this effect. It also addresses the issue of how the signal information to bind or unbind is transmitted through the protein. The model may be applicable to a wide range of repressors and also to signaling in trans-membrane proteins.     

Coarse-grained model of long-term supply of oil

The author proposes a coarse-grained kinetic model of the supply of oil during the next 50-year period. The oil supply, characterized by amount of oil extracted per day, is considered to depend on the oil price, existing capacities of oil extraction, the ability to find and develop new oil reserves, and also on the delay between investments and oil production. With reasonable parameters, the model predicts what may happen in realistic, optimistic, and pessimistic scenarios.     

A simple atomistic model for the simulation of the gel phase of lipid bilayers

In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two systems of different sizes ( 2×32 and 2×256 molecules), over a fairly large set of temperatures and densities, using parallel platforms and more standard serial computers. Depending on the dimension of the system, the dynamics was followed for physical times that go from few hundred picoseconds for the largest system to 5-10 nanoseconds for the smallest one. We find that the bilayer remains stable even in the absence of water and neglecting Coulomb interactions in the whole range of temperatures and densities we have investigated. The extension of the region of physical parameters that we have explored has allowed us to study significant points in the phase diagram of the bilayer and to expose marked structural changes as density and temperature are varied, which are interpreted as the system passing from a crystal to a gel phase. Received 6 July 2000 and Received in final form 28 December 2000     

The impact of model detail on power grid resilience measures

Extreme events are a challenge to natural as well as man-made systems. For critical infrastructure like power grids, we need to understand their resilience against large disturbances. Recently, new measures of the resilience of dynamical systems have been developed in the complex system literature. Basin stability and survivability respectively assess the asymptotic and transient behavior of a system when subjected to arbitrary, localized but large perturbations in frequency and phase. To employ these methods that assess power grid resilience, we need to choose a certain model detail of the power grid. For the grid topology we considered the Scandinavian grid and an ensemble of power grids generated with a random growth model. So far the most popular model that has been studied is the classical swing equation model for the frequency response of generators and motors. In this paper we study a more sophisticated model of synchronous machines that also takes voltage dynamics into account, and compare it to the previously studied model. This model has been found to give an accurate picture of the long term evolution of synchronous machines in the engineering literature for post fault studies. We find evidence that some stable fix points of the swing equation become unstable when we add voltage dynamics. If this occurs the asymptotic behavior of the system can be dramatically altered, and basin stability estimates obtained with the swing equation can be dramatically wrong. We also find that the survivability does not change significantly when taking the voltage dynamics into account. Further, the limit cycle type asymptotic behaviour is strongly correlated with transient voltages that violate typical operational voltage bounds. Thus, transient voltage bounds are dominated by transient frequency bounds and play no large role for realistic parameters.     

Classical many-body model for heavy-ion collisions incorporating the Pauli principle

A classical model for heavy-ion collisions, introduced previously, has been extended to include certain effects of the Pauli principle. All nucleons are treated equally. They obey classical dynamics and interact through an ordinary two-body force and through a momentumdependent two-body “Pauli core” which satisfies, approximately, that $\text{p}{}_{\mathrm{ij}}\text{r}{}_{\mathrm{ij}}\text{≧ξ}\text{h}\text{?}$, where ξ is a dimensionless constant. A form for the Pauli core is presented. The ordinary two-body force has been adjusted to fit bulk properties of nuclei and to reproduce that moment of nucleon nucleon scattering cross sections which is relevant to hydrodynamics. The parameters of the forces are given.     

Kinetic Monte Carlo simulations of heteroepitaxial growth with an atomistic model of elasticity

We have implemented Kinetic Monte Carlo (KMC) simulations of growth of heteroepitaxial thin films. A simple cubic Solid-on-Solid (SOS) model is used to describe the atomic configurations and nearest neighbor bonds are used to describe the energetics. Elastic effects are modeled using harmonic springs between atoms displaced from their lattice positions. The misfit strain is a consequence of different equilibrium spring lengths for the substrate and film. The consistency of this elastic model with continuum theories for strained surfaces has been shown by performing elastic energy calculations for various morphologies. KMC simulations for submonolayer deposition show scaling behavior in the island size distribution. The resulting island shapes are predominantly square and do not show any shape transitions in the physically relevant range of conditions. This method gives a detailed understanding of elastic interactions and their interplay with surface diffusion in heteroepitaxial systems.     

Investigation of a Kubo-formula-based approach to estimate DNA conductance in an atomistic model

A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can easily be extended to treat arbitrary chemical modifications of DNA.     

An agent-based model of stock markets incorporating momentum investors

It has been widely accepted that there exist investors who adopt momentum strategies in real stock markets. Understanding the momentum behavior is of both academic and practical importance. For this purpose, we propose and study a simple agent-based model of trading incorporating momentum investors and random investors. The random investors trade randomly all the time. The momentum investors could be idle, buying or selling, and they decide on their action by implementing an action threshold that assesses the most recent price movement. The model is able to reproduce some of the stylized facts observed in real markets, including the fat-tails in returns, weak long-term correlation and scaling behavior in the kurtosis of returns. An analytic treatment of the model relates the model parameters to several quantities that can be extracted from real data sets. To illustrate how the model can be applied, we show that real market data can be used to constrain the model parameters, which in turn provide information on the behavior of momentum investors in different markets.     

Prediction of the magnetotoroidic effect from atomistic simulations

An effective Hamiltonian technique is used to investigate the effect of applying curled electric fields on physical properties of stress-free BiFeO(3) dots being under open-circuit electrical boundary conditions. It is discovered that such fields can lead to a control of not only the magnitude but also the direction of the magnetization. Such control originates from the field-induced transformation or switching of electrical vortices and their couplings with oxygen octahedral tilts and magnetic dipoles. This control involves striking intermediate states and constitutes a novel phenomenon that can be termed a "magnetotoroidic" effect.     

Enhanced optical nonlinearities of superlattices within the Kronig-Penney model incorporating inherent bulk nonlinearities

Third order nonlinear optical susceptibilities χ⁽³⁾ of GaAs/Ga_1?xAlAs superlattices have been predicted which are two orders of magnitude larger than those of bulk GaAs. This enhancement is due to the band nonparabolicity arising from the additional periodicity of the superlattice. These predictions, based on a tight-binding model of the superlattice dispersion, are here extended to the more realistic Kronig-Penney (KP) model. Corrections to tight-binding are non-negligible; however, enhancements of χ⁽³⁾ are still large but reduced approximately 30%–50% over previous estimates. The KP model is also here applied to superlattices employing InSb as the quantum well material. Because of the smaller effective mass of InSb, and taking account of its bulk nonparabolicity, the minibands move to higher energy, enhancing the interwell overlap and increasing χ⁽³⁾ by about one order of magnitude over that of bulk InSb. The role of the barrier material in this case is important and is discussed. The interplay between the bulk nonparabolicity and that arising from the superlattice is also addressed.     

Coarse-grained Hamiltonian description of the Breit-Darwin plasma close to equilibrium

The coarse-grained approximation is shown to be a convenient tool of handling the many-body interactions inherent in the hamiltonian formulation of the Breit-Darwin plasma. A linear kinetic equation compatible with previous results is found. The equilibrium binary correlation is corrected.     

Lattice tube model of proteins

We present a new lattice model for proteins that incorporates a tubelike anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins.     

A novel Monte Carlo scheme for the rapid equilibration of atomistic model polymer systems of precisely defined molecular architecture

Two novel connectivity-altering atomistic Monte Carlo moves are presented for the fast equilibration of condensed phases of long-chain systems with a variety of chain architectures. With the new moves, isotropic or oriented melts of linear or long-chain branched polymers, dense brushes of terminally grafted macromolecules, and cyclic peptides can be simulated. Results concerning the structural, conformational, and volumetric properties of linear, monodisperse polyethylene melts, simulated with a new united-atom molecular model, are in excellent agreement with experimental data.     

Structural role of the copper ions in the dinuclear active site of Carcinus aestuarii hemocyanin

In this work we show, by a combination of biochemical and biophysical approaches, that the copper ions bound in the binuclear active site of Carcinus aestuarii hemocyanin play a stabilizing role on the tertiary structure of the protein. Upon removal of copper, the monomeric hemocyanin, but not the hexameric oligomer, undergoes changes at the level of tertiary structure while the secondary structure is almost unaffected. By Small-Angle X-Ray Scattering, supported by gel chromatography measurements, it can be concluded that the apo-monomer, but not the holo form or the hexameric form, undergoes a slow time-dependent oligomerization process.     

活性蓄冷器数学模型的研究进展

活性蓄冷器是室温磁制冷机的核心部分,它的性能直接影响整个磁制冷系统。了解其工作机理和热力学特性对制冷机的设计与优化具有重要意义。综述了近年来活性蓄冷器数学模型的研究进展,并对模型进行了比较分析。     

Atomistic simulation of the transition from atomistic to macroscopic cratering

Using large-scale atomistic simulations, we show that the macroscopic cratering behavior emerges for projectile impacts on Au at projectile sizes between 1000 and 10000 Au atoms at impact velocities comparable to typical meteoroid velocities. In this size regime, we detect a compression of material in Au nanoparticle impacts similar to that observed for hypervelocity macroscopic impacts. The simulated crater volumes agree with the values calculated using the macroscopic crater size scaling law, in spite of a downwards extrapolation over more than 15 orders of magnitude in terms of the impactor volume. The result demonstrates that atomistic simulations can be used as a tool to understand the strength properties of materials in cases where only continuum models have been possible before.     

Saltatory waves in the spike-diffuse-spike model of active dendritic spines

In this Letter we present the explicit construction of a saltatory traveling pulse of nonconstant profile in an idealized model of dendritic tissue. Excitable dendritic spine clusters, modeled with integrate-and-fire (IF) units, are connected to a passive dendritic cable at a discrete set of points. The saltatory nature of the wave is directly attributed to the breaking of translation symmetry in the cable. The conditions for propagation failure are presented as a function of cluster separation and IF threshold.