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납본여부: 미납본

Supercomputing and Beyond

비매품/무

Changes in power spectrum of R-R interval variability during general anesthesia : Real time analysis and monitoring system

학위논문(박사)--서울대학교 대학원 :의학과 마취과학전공,1995.Docto

Nanoscale Spiral Flow in a Cylindrical Channel

We study the behavior of pressure-driven flow in a cylindrical nanochannel patterned with different wettability using molecular dynamics simulations. We consider the flow perpendicular or parallel to the periodic stripes of wetting and nonwetting materials. For both geometries, we observe a sharp increase in the longitudinal velocity of the flow as wetting stripe width decreases, which is clearly distinguishable from the case of shear-driven flow. When the channel wall is spirally patterned with distinct wetting stripes, the transverse velocity of the flow is generated in the channel and its generation depends strongly on the degree of molecular ordering above the wetting stripes, which can be controlled by helical angle, wetting stripe width, the relative area of the wetting region, and the strength of the fluid-wall interaction

Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics, and how they interact

Chromosomes in living cells are strongly con?ned but show a high level of spatial organization. Similarly, con?ned polymers display intriguing organizational and segregational properties. Here, we discuss how ring topology in?uences self-avoiding polymers con?ned in a cylindrical space, i.e. individual polymers as well as the way they interact. Our molecular dynamics simulations suggest that a ring polymer can be viewed as a parallel connection of two linear subchains, each trapped in a narrower imaginary tube. As a consequence, ring topology stiffens individual chains about ?vefold and enhances their segregation appreciably, as if it induces extra linear ordering. Using a renormalized Flory approach, we show how ring topology in?uences individual chains in the long chain limit. Our polymer model quantitatively explains the long-standing observations of chromosome organization and segregation in E. coli

Interchain ordering and segregation of polymers under confinement

Westudytherelationshipbetweenintrachainorderingandsegregationtendencyoftwopolymersconfinedinacylindricalspace.WefindthechainssegregatespontaneouslyevenoutsidedeGennes’linear-orderingscalingregime,inwhicheachchainisalineararrayofblobs.Whenthechainsareweaklycompressedagainsteachother,linearorderingiswellpreservedandthechainsremainsegregated

Elasticity of Flexible Polymers under Cylindrical Confinement: Appreciating the Blob Scaling Regime in Computer Simulations

Despite much renewed interest in cylindrically confined polymers with linear or nonlinear topology, often considered as model chromosomes, their scaling predictions, especially on chain elasticity and relaxation, have not been reconciled with numerical data. Of particular interest is their “effective spring constant” given in the scaling form of keff ∼ N−αD−γ, where N is the number of monomers and D the diameter of the cylindrical space. If the blob-scaling approach produces α = 1 and γ = 2 − 1/ν = 1/3 with ν = 3/5 the Flory exponent, a series of numerical studies indicate α ≈ 0.75 and unexpectedly large γ ≈ 0.9. Using computer simulations, we show that there exists a crossover from the formerly called unexpected to blob-scaling regime at a certain value of D ≈ 10 (in units of monomer sizes) for sufficiently large N (>Ncr). Our results suggest that Ncr ≈ 1000, if the farthermost distance is used as the chain size: a quantity relevant in single-chain manipulations or for ring polymers (e.g., bacterial chromosomes). Accordingly, chain relaxation dynamics is expected to show a similar crossover. Our results imply that the applicability of the blob scaling approach depends on how confined chains are characterized

Polymers under confinement: single polymers, how they interact, and as model chromosomes

How confinement or a physical constraint modifies polymer chains is not only a classical problem in polymer physics but also relevant in a variety of contexts such as single-molecule manipulations, nanofabrication in narrow pores, and modelling of chromosome organization. Here, we review recent progress in our understanding of polymers in a confined (and crowded) space. To this end, we highlight converging views of these systems from computational, experimental, and theoretical approaches, and then clarify what remains to be clarified. In particular, we focus on exploring how cylindrical confinement reshapes individual chains and induces segregation forces between them – by pointing to the relationships between intra-chain organization and chain segregation. In the presence of crowders, chain molecules can be entropically phase-separated into a condensed state. We include a kernel of discussions on the nature of chain compaction by crowders, especially in a confined space. Finally, we discuss the relevance of confined polymers for the nucleoid, an intracellular space in which the bacterial chromosome is tightly packed, in part by cytoplasmic crowder

Overlapping two self-avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell

We study the spatial organization and segregation of two self-avoiding polymers trapped inside a closed cylindrical pore. Using molecular dynamics simulations, we show how confinement shapes the chains, especially their mutual (entropic) force, chain miscibility, and segregation dynamics. Under strong confinement, the chains are shown to repel more strongly and thus segregate better, if they are shorter and the confining space is more asymmetric

Molecular dynamics on nonequilibrium motion of a colloidal particle driven by an external torque

We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use molecular dynamics simulation as an alternative to the Langevin dynamics. We prepare a heat bath composed of thousands of particles interacting with each other through the Lennard–Jones potential and impose the Langevin thermostat to maintain the heat bath in equilibrium. We consider a single colloidal particle interacting with with the particles of the heat bath also by the Lennard–Jones potential, without applying any types of dissipative or fluctuating forces used in Langevin dynamics. We set up simulation protocol fit for the overdamped limit as in real experiments, by increasing the size and mass of the colloidal particle. We study nonequilibrium fluctuations for work and heat produced incessantly in time and compare the results with those obtained from the previous studies via the overdamped Langevin dynamics. We confirm the Gallavotti–Cohen symmetry and the fluctuation theorem