Single chain force spectroscopy - Reading the sequence of HP protein models

We study the elastic properties of single A/B random copolymer chains, with a specific sequence and use them as theoretical model for so called HP proteins. HP proteins carry hydrophilic (P) and hydrophobic (H) monomers. We predict a rich structure in the force-extension relations which can be attributed to the information in the sequence. The variational method is used to probe local minima on the path of stretching and releasing for the chain molecules. At a given force, we find multiple configurations which are separated by energy barriers. A collapsed globular configuration consists of several domains which unravel cooperatively. Upon stretching, the unfolding path shows a stepwise pattern corresponding to the unfolding of each domain. While releasing, several cores can be created simultaneously in the middle of the chain, resulting in a different path of collapse. The long-range interactions and stiffness of the chain simplify the potential landscape given by the disorder in sequence. Received 5 March 2002 / Received in final form 16 May 2002 Published online 13 August 2002     

Controlling global stochasticity of Hamiltonian systems by nonlinear perturbation

A method of controlling global stochasticity in Hamiltonian systems by applying nonlinear perturbation is proposed. With the well-known standard map we demonstrate that this control method can convert global stochasticity into regular motion in a wide chaotic region for arbitrary initial condition, in which the control signal remains very weak after a few kicks. The system in which chaos has been controlled approximates to the original Hamiltonian system, and this approach appears robust against small external noise. The mechanism underlying this high control efficiency is intuitively explained. Received 15 January 2002 Published online 6 June 2002     

Numerical simulation of the spatiotemporal evolution of a nanoparticle–plasma system

A one-dimensional nanodusty plasma was modeled by self-consistently coupling a plasma model with nanoparticle growth, charging, and transport models. As nanoparticles grow from subnanometer to tens of nm in diameter, the numerical results predict a rich spatiotemporal structure, including four distinct temporal phases: a charge-limited phase, a charge accumulation phase, an early ion drag phase, and a sheath interaction phase.     

Molecular dynamics simulations on the structures and properties of ε-CL-20-based PBXs ——Primary theoretical studies on HEDM formulation design

Five polymer bonded explosives (PBXs) with the base explosive ε-CL-20 (hexanitrohexaazaisowurtzi- tane), the most important high energy density compound (HEDC), and five polymer binders (Estane 5703, GAP, HTPB, PEG, and F2314) were constructed. Molecular dynamics (MD) method was employed to investigate their binding energies (Ebind), compatibility, safety, mechanical properties, and energetic properties. The information and rules were reported for choosing better binders and guiding formula- tion design of high energy density material (HEDM). According to the calculated binding energies, the ordering of compatibility and stability of the five PBXs was predicted as ε-CL-20/PEG > ε-CL-20/ Estane5703 ≈ε-CL-20/GAP > ε-CL-20/HTPB > ε-CL-20/F2314. By pair correlation function g(r) analyses, hydrogen bonds and vdw are found to be the main interactions between the two components. The elasticity and isotropy of PBXs based ε-CL-20 can be obviously improved more than pure ε-CL-20 crystal. It is not by changing the molecular structures of ε-CL-20 for each binder to affect the sensitivity. The safety and energetic properties of these PBXs are mainly influenced by the thermal capability (C°p) and density (ρ) of binders, respectively.     

Biham–Middleton–Levine model with four-directional traffic

We study the four-directional traffic flow on a two-dimensional lattice. In the case of discrete densities, we assume equal number of vehicles in each lane. Except for the minimum density, the gridlock emerges swiftly. Two kinds of gridlock have been observed. The global gridlock dominates the system when the density is twice the minimum value. At higher densities, the system is pervaded by local gridlocks. We also analyze the time evolution of average speed. In the case of continuous densities, the vehicle numbers vary from lane to lane. The global gridlock is then destroyed by the fluctuations; while the local gridlock can still be observed.     

Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed     

Evolution in complex systems

What features characterize complex system dynamics? Power laws and scale invariance of fluctuations are often taken as the hallmarks of complexity, drawing on analogies with equilibrium critical phenomena. Here we argue that slow, directed dynamics, during which the system's properties change significantly, is fundamental. The underlying dynamics is related to a slow, decelerating but spasmodic release of an intrinsic strain or tension. Time series of a number of appropriate observables can be analyzed to confirm this effect. The strain arises from local frustration. As the strain is released through “quakes,” some system variable undergoes record statistics with accompanying log‐Poisson statistics for the quake event times. We demonstrate these phenomena via two very different systems: a model of magnetic relaxation in type II superconductors and the Tangled Nature model of evolutionary ecology and show how quantitative indications of aging can be found. © 2004 Wiley Periodicals, Inc. Complexity 10: 49–56, 2004     

Creation, Dissipation and Recycling of Resources in Non-Equilibrium Systems

In this article, we define stochastic dynamics for a system coupled to reservoirs. The rules for forward and backward transitions are related by a generalized detailed balance identity involving the system and its reservoirs. We compare the variation of information and of entropy. We define the Carnot dissipation and prove that it can be expressed in terms of cyclic transformations. Lower bounds for partial dissipations are also studied, as well as the effect of switching off certain reservoirs. We also study the near degeneracy of the stochastic matrix, relate it to phase transitions and we show that the reduced dynamics on the set of phases is a permutation. Finally, we relate these concepts to heat, work and more generally to the dissipation and creation of resources, in general systems.     

利用弧形光栅尺测量大型转轴扭矩的原理研究

利用弧形光栅尺的旋转微位移测量功能,组建一组测量体系,用于测量巨型转轴的扭矩。采用四组相同的弧形光栅尺同时测量两截面的相对转角,通过多点测量实现误差均化,得出了消除转轴直径对测量影响的公式,使仪器的环境适应能力得到了极大地提高。根据不同的工作情况,提出了相应的动态测量扭矩的计算方程。实现了大型机械设备主传动的动力监测,为设备自动化、智能化奠定了基础。     

A computational strategy for multiscale systems with applications to Lorenz 96 model

Numerical schemes for systems with multiple spatio-temporal scales are investigated. The multiscale schemes use asymptotic results for this type of systems which guarantee the existence of an effective dynamics for some suitably defined modes varying slowly on the largest scales. The multiscale schemes are analyzed in general, then illustrated on a specific example of a moderately large deterministic system displaying chaotic behavior due to Lorenz. Issues like consistency, accuracy, and efficiency are discussed in detail. The role of possible hidden slow variables as well as additional effects arising on the diffusive time-scale are also investigated. As a byproduct we obtain a rather complete characterization of the effective dynamics in Lorenz model.