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A ten Bosch
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ABSTRACT: Dynamic and structural properties of biological polymers are important to their function but it is difficult to obtain information on molecular flexibility at an atomic level. This paper describes how a normal mode analysis can be used to describe the equilibrium and nonequilibrium properties of complex polymer systems such as DNA in solution. A weak coupling between the chain deformation and the local chain orientation simplifies the calculations. A crossover in the normal mode behavior is proposed with a transition from straight rod bend modes to longitudinal oscillations of a coil conformation as a function of the stiffness and the degree of polymerization.
The Journal of chemical physics 04/2011; 134(13):134902. · 3.09 Impact Factor
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ABSTRACT: The voltage-driven dynamics of a stiff polymer through a nanopore are treated with a bend elastic model. In contrast to flexible polymers described by a stretch elasticity, bend elastic chains can be oriented in an external field, here the anchoring field created by the pore atoms. The trajectory of the chain is calculated using the Langevin equation of motion. The dynamical equation is solved by a normal mode analysis of the elastic curve with free ends. Interaction with the pore walls acts to align the chain, and with the electric field induced inside the pore controls the translocation time. Application of a force proportional to the distance of the exit from the end of the pore such as an optical trap slows down the motion, and reduces the chain response to the wall potential and the extension along the pore axis. DNA is a well-known semirigid polymer, and a comparison is made to the molecular dynamics simulation of translocation of DNA through a synthetic nanopore.
Physical Review E 02/2009; 79(1 Pt 1):011903. · 2.26 Impact Factor
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A. ten Bosch
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ABSTRACT: The voltage-driven dynamics of a stiff polymer through a nanopore are treated with a bend elastic model. In contrast to flexible polymers described by a stretch elasticity, bend elastic chains can be oriented in an external field, here the anchoring field created by the pore atoms. The trajectory of the chain is calculated using the Langevin equation of motion. The dynamical equation is solved by a normal mode analysis of the elastic curve with free ends. Interaction with the pore walls acts to align the chain, and with the electric field induced inside the pore controls the translocation time. Application of a force proportional to the distance of the exit from the end of the pore such as an optical trap slows down the motion, and reduces the chain response to the wall potential and the extension along the pore axis. DNA is a well-known semirigid polymer, and a comparison is made to the molecular dynamics simulation of translocation of DNA through a synthetic nanopore.
Phys. Rev. E. 01/2009; 79(1).
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A ten Bosch
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ABSTRACT: Small scale particle motion is the cause of dynamic roughening and plays a role during film growth. To study surface waves on the molecular level, a continuum approach is used that links atomic and macroscopic dynamics though a Fokker-Planck equation for the distribution of particle trajectories. The dynamic equation for the density interfacial profile includes inertia terms indispensable for high frequency fluctuations. For wave vectors below the critical value, an initial periodic deformation of the surface on the order of the density correlation length simply decays with time. Above the critical wave vector, collective periodic motion is induced in the interface. A picture of short lived, localized high frequency wavelets emerges with contributions from acoustic, capillary, and elastic surface modes.
Physical Review E 04/2006; 73(3 Pt 1):031605. · 2.26 Impact Factor
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A ten Bosch
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ABSTRACT: Conditions for surface nucleation and growth of a film are determined in a diffuse interface model. A method is given, derived from a Fokker-Planck equation for the nonequilibrium particle distribution, which links atomic and mesoscopic events in a rheological description similar to the classical continuum theory of fluid flow. Film nucleation and growth are modeled by the spatially inhomogeneous continuous evolution of the instantaneous density profile which measures the average number of particles or molecules at given time and position. It is shown how an alteration in the distribution of particles in the vicinity of the boundary between parent and product phases induces transient film growth and damped vibrations at the surface. The method is general but as an illustration, the condensation of a simple classical fluid on cooling is considered in detail.
Physical Review E 04/2006; 73(3 Pt 1):031606. · 2.26 Impact Factor
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A ten Bosch
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ABSTRACT: Kinetic mesoscopic theory derived from an atomistic model is applied to study permeation and separation of gases in a single rectangular pore. The goal is to judge the analytical method against the results of molecular dynamics simulation and to demonstrate the ease and relevance of analytical theories to calculate density profiles, flux, permeance, and separation factors. The permeance is linked to the amount of gas adsorbed in the pore and the effect of the effective gas-wall interaction on adsorption is explored. The effects of pore size, temperature, and the parameters of the pore wall interaction are investigated and reproduce the trends found in the numerical simulation of permeation of a mixture of methane and carbon dioxide in a carbon nanopore.
The Journal of Chemical Physics 03/2005; 122(8):84711. · 3.33 Impact Factor
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A ten Bosch
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ABSTRACT: The dynamics of single particles in a cluster on condensation from the supersaturated vapor phase is studied by a kinetic approach. An insight into the distinctive flow field in the vicinity of a cluster is obtained for initial and late stage evolution. Inside the core the single atoms diffuse freely and the initial velocity decays rapidly with time. In the interfacial region between the cluster core and the vapor, the surface pressure produces a directed radial motion and a long time radial drift into the cluster core. Far from the cluster, the atoms move in the vapor state of low density and high diffusion constant. The mean square displacement and the velocity correlation lend support to the results and are compared with recent molecular dynamics simulations on a nucleating argon cluster.
Physical Review E 05/2003; 67(4 Pt 1):041602. · 2.26 Impact Factor
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A ten Bosch
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ABSTRACT: In the present paper, the simultaneous effect on a polymer of orientation by a solid surface and strong repulsion at the interface with an incompatible liquid is studied. Semiflexible polymers resist deformations perpendicular to the monomer and have a tendency to align in a given direction in contact with a surface. When a second incompatible liquid is added, a sharp interface between the two liquids forms at a given distance from the substrate. By changing the nature of the second liquid, this second constraint can control the order and force the polymer in the ordered surface layer to assume different conformations. The wormlike chain is used to define the parameters of the system that will determine the resulting conformation. An extended or contracted form is found depending on how the chains interact with the liquid.
Physical Review E 07/2001; 63(6 Pt 1):061808. · 2.26 Impact Factor
