Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes

Using a coarse-grained molecular dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling or emptying carbon nanotubes as a function of system parameters. Different levels of the pore hydrophobicity give rise to tubes that are empty, water-filled, or fluctuate between these two long-lived metastable states. The corresponding coarse-grained free-energy surfaces and their hysteretic parameter dependence are explored by linking MD to continuum fixed point and bifurcation algorithms. The results are validated through equilibrium MD simulations.     

Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that ≈40-base molecules can undergo kinetic transitions between two well-defined “open” and “closed” states, on a timescale ≈1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed. Our dynamical model is also applied to the unzipping of long (kilo-basepair) DNA molecules at constant force. Received 29 July 2002 / Received in final form 5 February 2003 Published online: 16 April 2003 RID="a" ID="a"e-mail: cocco@ldfc.u-strasbg.fr RID="b" ID="b"e-mail: jmarko@uic.edu RID="c" ID="c"e-mail: monasson@lpt.ens.fr     

Computational determination of radiation damage effects on DNA structure

Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.     

Insights into the Discrepancy between Single Molecule Experiments

Sharp bending as one of the mechanical properties of double-stranded DNA(dsDNA) on the nanoscale is essential for biological functions and processes. Force sensors with optical readout have been designed to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA(ssDNA). Recent FRET singlemolecule experiments were carried out based on the same force sensor design, but provided totally contrary results. In the current work, Monte Carlo simulations were performed under three conditions to clarify the discrepancy between the two experiments. The criterion that the work done by the force exerted on dsDNA by ssDNA should be larger than the nearest-neighbor(NN) stacking interaction energy is used to identify the generation of the fork at the junction of dsDNA and ssDNA. When the contour length of dsDNA in the sensor is larger than its critical length, the fork begins to generate at the junction of dsDNA and ssDNA, even with a kink in dsDNA. The forces inferred from simulations under three conditions are consistent with the ones inferred from experiments, including extra large force and can be grouped into two different states, namely, fork states and kink states. The phase diagrams constructed in the phase space of the NN stacking interaction energy and excited energy indicate that the transition between the fork state and kink state is difficult to identify in the phase space with an ultra small or large number of forks, but it can be detected in the phase space with a medium number of forks and kinks.     

Wave propagation of nonlinear modes and formation of bubble in a two-component helicoidal lattice

Through the multiplescale expansion, we show that the dynamics of modulated waves in atwo-component helicoidal one-dimensional model is governed by thenonlinear Schrödinger (NLS) equation. We study the occurrence ofpatterns formation in such a system. The impact of the helicoidalcoupling is also studied which reveals that high values of thehelicoidal coupling constant contribute to regulate information andcharge transport throughout the two-chain model. This is madepossible due to the superposition of optical and acoustic modes. Inaddition, the model is used to investigate internal dynamics of DNA.It is shown that the opening of the double helix of the DNA itselfis controlled by the resonance mode, where the unzipping of thedouble helix has been illustrated by numerical simulations.Furthermore, the shape of the eyelike shape previously observed inexperiments of thermal denaturation of DNA is numerically obtained.     

Observation of three-dimensional long-range order in small ion coulomb crystals in an rf trap

Three-dimensional long-range ordered structures in smaller and near-spherically symmetric Coulomb crystals of (40)Ca(+) ions confined in a linear rf Paul trap have been observed when the number of ions exceeds approximately 1,000 ions. This result is unexpected from ground state molecular dynamics (MD) simulations, but found to be in agreement with MD simulations of metastable ion configurations. Previously, three-dimensional long-range ordered structures have only been reported in Penning traps in systems of approximately 50,000 ions or more.     

Classical Molecular Dynamics Model for Coupled Two‐Component Plasmas – Ionization Balance and Time Considerations

The dynamic properties of ion‐electron two‐component plasmas (TCP) are studied by using classical molecular dynamics (MD) simulations. There is a variety of time dependent and structural results that MD is able to provide in complement to other methods, e.g., useful micro‐field sequences can be generated. The method deals with some specific difficulties: the mass ratio between ions and electrons enforces very small time‐steps appropriate to follow electrons motion while, ions must move significantly in order to build, self consistently, their spatial structure. This results in expensive simulations. Electron trajectories are trapped and de‐trapped with multiple electron collisions around ions resulting in the occurrence of quasi metastable bound electron states. An analysis of micro‐fields at neutral in a hydrogen plasma reveals the need to consider a complete hierarchy of time scales extended typically over 7 order of magnitude, i.e., from a time‐step: ～10^‐19s, to a time required to obtain statistical averages, ～10^‐11s. In order to extend the MD capabilities in representing real coupled plasmas a classical ionization/recombination process has been implemented allowing to follow the evolution of plasmas involving several ion stages and model the ionization balance. Here again TCP simulations deal with extended time‐scale providing information about relaxation of non equilibrium plasma states (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Adhesive emulsion bilayers under an electric field: from unzipping to fusion

Water-in-oil emulsion drops are formed and stabilized with phospholipids which can adhere and form a bilayer. Using microfluidics, adhesive drop pairs are then trapped and submitted to an ac electric field. We observe three distinct states as a function of the adhesion energy and the electric field intensity. The pair can be either stable, though slightly deformed, or unzip and separate, or coalesce. The frontiers between the different states directly reflect vesicle detachment forces and electroporation theories. The experimental approach that we propose for probing liquid interface wetting between monolayers allows us to finely tuned the tension in the bilayer and gives access to bilayer unzipping.     

水高温高密度状态方程理论研究

 采用MCR方法计算由exp-6势描述的水分子作用体系的pVT状态方程。与MD数值模拟结果比较后发现，由于水分子间强烈的吸引作用有利于分子有序化过程的发生，在较高温度（2 000~4 000 K）条件下，水分子作用体系仍呈现出固态特征。该物相区内体系的热力学性质不能用MCR理论描述但MCR理论准确预言了水分子作用体系高温液相区pVT状态方程。     

Supercooled superfluids in Monte Carlo simulations

We perform path integral Monte Carlo simulations to study the imaginary time dynamics of metastable supercooled superfluid states and nearly superglassy states of a one component fluid of spinless bosons square wells. Our study shows that the identity of the particles and the exchange symmetry is crucial for the frustration necessary to obtain metastable states in the quantum regime. Whereas the simulation time has to be chosen to determine whether we are in a metastable state or not, the imaginary time dynamics tells us if we are or not close to an arrested glassy state.     

Molecular motion in restricted geometries

Molecular dynamics in restricted geometries is known to exhibit anomalous behaviour. Diffusion, translational or rotational, of molecules is altered significantly on confinement in restricted geometries. Quasielastic neutron scattering (QENS) offers a unique possibility of studying molecular motion in such systems. Both time scales involved in the motion and the geometry of motion can be studied using QENS. Molecular dynamics (MD) simulation not only provides insight into the details of the different types of motion possible but also does not suffer limitations of the experimental set-up. Here we report the effect of confinement on molecular dynamics in various restricted geometries as studied by QENS and MD simulations. An example where the QENS technique provided direct evidence of phase transition associated with change in the dynamical behaviour of the molecules is also discussed.      

Dynamic Behavior of a Spin- 1 Ising Model. I. Relaxation of Order Parameters and the “Flatness” Property of Metastable States

The dynamic behavior of a spin-1 Ising system with arbitrary bilinear and biquadratic pair interactions is studied by using the path probability method, and approaches of the system toward the stable or metastable equilibrium states according to the ratio of interaction parameters and rate constants are presented. In particular, we investigate the relaxation of the order parameters for temperatures less than, equal to, and greater than the second-order and first-order phase transitions. From this investigation, the “flatness” property of metastable states is seen explicitly. We also show how a system freezes in a metastable state as well as how it escapes from one metastable state to the other.     

高压下Fe从bcc到hcp结构相变机理的第一性原理计算

采用基于密度泛函理论的第一性原理方法, 分别研究了压力作用下Fe从体心立方 (bcc,α 相) 结构到六角密排(hcp, ε相) 结构相变的两种不同的相变机理: 相变过程中出现亚稳定的面心立方(fcc) 结构(bcc-fcc-hcp) , 以及相变过程中没有出现亚稳定的fcc结构(bcc-hcp) . 计算结果表明: 静水压力条件下, 相变过程中并不会产生亚稳定的fcc结构, 这与最近的原位XRD实验测量结果相一致. 随着压力的增加, fcc-hcp的相变势垒逐渐增加, 压力趋向于阻止Fe从fcc结构到hcp结构的相变. 计算得到了相变过程中原子磁性和结构的详细信息, 分析表明相变过程中涉及复杂的磁性转变, 并且讨论了原子磁性对结构转变影响的物理机理. 此外, 对分子动力学模拟中产生亚稳定的fcc结构的原因也进行了讨论. 关键词： 相变机理 静水压力 第一性原理 铁     

Unzipping kinetics of double-stranded DNA in a nanopore

We studied the unzipping of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. Polymerase chain reaction analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.     

Measurements of argon metastable density using the tunable diode laser absorption spectroscopy in Ar and Ar/O_2

Densities of Ar metastable states 1s_5 and 1s_3 are measured by using the tunable diode laser absorption spectroscopy(TDLAS) in Ar and Ar/O2 mixture dual-frequency capacitively coupled plasma(DF-CCP). We investigate the effects of high-frequency(HF, 60 MHz) power, low-frequency(LF, 2 MHz) power, and working pressure on the density of Ar metastable states for three different gas components(0%, 5%, and 10% oxygen mixed in argon). The dependence of Ar metastable state density on the oxygen content is also studied at different working pressures. It is found that densities of Ar metastable states in discharges with different gas components exhibit different behaviors as HF power increases. With the increase of HF power, the metastable density increases rapidly at the initial stage, and then tends to be saturated at a higher HF power. With a small fraction(5% or 10%) of oxygen added in argon plasma, a similar change of the Ar metastable density with HF power can be observed, but the metastable density is saturated at a higher HF power than in the pure argon discharge. In the DF-CCP, the metastable density is found to be higher than in a single frequency discharge, and has weak dependence on LF power. As working pressure increases, the metastable state density first increases and then decreases,and the pressure value, at which the density maximum occurs, decreases with oxygen content increasing. Besides, adding a small fraction of oxygen into argon plasma will significantly dwindle the metastable state density as a result of quenching loss by oxygen molecules.     

Stable and metastable states and the formation and destruction of breathers in the discrete nonlinear Schrödinger equation

Statistical mechanics explains many localization phenomena of lattices such as the discrete nonlinear Schrödinger equation. However, numerical simulations show that the complete thermalization is rarely achieved. Instead, one observes metastable statistical states that are robust when excited locally. This paper investigates thermodynamically metastable states where the trajectory is confined to some part of the energy shell. The partition function and the entropy are computed with a perturbation method. This method is applicable to stable and metastable states, and it allows us to give approximative analytic expressions for the entropy in the complete thermodynamic state space.     

Metastable molecular fluid hydrogen at high pressures

Warm dense hydrogen is studied in the region of fluid–fluid phase transition within the framework of the density functional theory. We report a procedure of obtaining metastable states and calculate the equation of state. Metastable states are diagnosed by pair correlation functions and values of conductivity. We obtain a strong overlapping through the density of metastable and equilibrium branches of pressure isotherms. This indicates the plasma nature of the phase transition.     

Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation

Single-molecule experiments on polymeric DNA show that the molecule can be overstretched at nearly constant force by about 70% beyond its relaxed contour length. In this publication we use steered molecular dynamics (MD) simulation to study the effect of structural defects on force-extension curves and structures at high elongation in a 30 base pair duplex pulled by its torsionally unconstrained 5' -5' ends. The defect-free duplex shows a plateau in the force-extension curve at 120pN in which large segments with inclined and paired bases (“S-DNA”) near both ends of the duplex coexist with a central B-type segment separated from the former by small denaturation bubbles. In the presence of a base mismatch or a nick, force-extension curves are very similar to the ones of the defect-free duplex. For the duplex with a base mismatch, S-type segments with highly inclined base pairs are not observed; rather, the overstretched duplex consists of B-type segments separated by denaturation bubbles. The nicked duplex evolves, via a two-step transition, into a two-domain structure characterized by a large S-type segment coexisting with several short S-type segments which are separated by short denaturation bubbles. Our results suggest that in the presence of nicks the force-extension curve of highly elongated duplex DNA might reflect locally highly inhomogeneous stretching.