Search Results - "Klenin, K"

Brownian Dynamics Simulation of DNA Unrolling from the Nucleosome by Wocjan, T, Klenin, K, Langowski, J

“…Nucleosomes organize chromatin in eukaryotic cells at the lowest scale by wrapping the DNA double helix around a histone octamer. The mechanism by which this…”
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SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems by Strunk, T., Wolf, M., Brieg, M., Klenin, K., Biewer, A., Tristram, F., Ernst, M., Kleine, P. J., Heilmann, N., Kondov, I., Wenzel, W.

“…Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family of Monte Carlo…”
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Conformational and thermodynamic properties of supercoiled DNA by Vologodskii, A V, Levene, S D, Klenin, K V, Frank-Kamenetskii, M, Cozzarelli, N R

“…We used Monte Carlo simulations to investigate the conformational and thermodynamic properties of DNA molecules with physiological levels of supercoiling…”
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Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study by Klenin, K.V., Frank-Kamenetskii, M.D., Langowski, J.

“…A Monte Carlo model for the generation of superhelical DNA structures at thermodynamic equilibrium (Klenin et al., 1991; Vologodskii et al., 1992) was modified…”
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Computer simulation of DNA supercoiling by Klenin, K V, Vologodskii, A V, Anshelevich, V V, Dykhne, A M, Frank-Kamenetskii, M D

“…We treat supercoiled DNA within a wormlike model with excluded volume. A modified Monte Carlo approach has been used, which allowed computer…”
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All-Atom Protein Folding with Free-Energy Forcefields by Verma, A., Gopal, S.M., Schug, A., Herges, T., Klenin, K., Wenzel, W.

“…Proteins are the workhorses of all cellular life. They constitute the building blocks and the machinery of all cells. DNA carries the genetic information which…”
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Looping Dynamics of Linear DNA Molecules and the Effect of DNA Curvature: A Study by Brownian Dynamics Simulation by Merlitz, Holger, Rippe, Karsten, Klenin, Konstantin V., Langowski, Jörg

“…A Brownian dynamics (BD) model described in the accompanying paper (Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the…”
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The diameter of the DNA superhelix decreases with salt concentration: SANS measurements and Monte Carlo simulations by Hammermann, M., Brun, N., Klenin, K.V., May, R. P., Tóth, K., Langowski, Jorg

“…We have measured the static form factor of superhelical DNA by SANS in dilute aqueous solution as a function of salt concentration. Theoretical static form…”
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Salt-Dependent DNA Superhelix Diameter Studied by Small Angle Neutron Scattering Measurements and Monte Carlo Simulations by Hammermann, Markus, Brun, Nathalie, Klenin, Konstantin V., May, Roland, Tóth, Katalin, Langowski, Jörg

“…Using small angle neutron scattering we have measured the static form factor of two different superhelical DNAs, p1868 (1868 bp) and pUC18 (2686 bp), in dilute…”
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Intrachain Reactions of Supercoiled DNA Simulated by Brownian Dynamics by Klenin, Konstantin V., Langowski, Jörg

“…We considered an irreversible biochemical intrachain reaction of supercoiled DNA as a random event that occurs, with certain probability, at the instant of…”
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DNA curvature influences the internal motions of supercoiled DNA by Kremer, W., Klenin, K., Diekmann, S., Langowski, J.

“…We present evidence that short curved DNA segments can act as mediators for the ordering of large domains in superhelical DNA. Using a non‐invasive solution…”
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Diffusion-Controlled Intrachain Reactions of Supercoiled DNA: Brownian Dynamics Simulations by Klenin, Konstantin V., Langowski, Jörg

“…The Brownian Dynamics technique was used to model a diffusion-controlled intramolecular reaction of supercoiled DNA (2500 basepairs) in 0.1 M sodium chloride…”
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Effect of excluded volume on topological properties of circular DNA by Klenin, K V, Vologodskii, A V, Anshelevich, V V, Dykhne, A M, Frank-Kamenetskii, M D

“…We have performed computer simulations of closed polymer chains with allowance for the excluded volume effects within the framework of the free-joint model…”
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Computation of writhe in modeling of supercoiled DNA by Klenin, Konstantin, Langowski, Jörg

“…We describe four previously unpublished methods allowing the computation of the writhe for a supercoiled DNA molecule modeled by a polymer chain consisting of…”
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Kinetics of antigen binding to antibody microspots: Strong limitation by mass transport to the surface by Kusnezow, Wlad, Syagailo, Yana V., Rüffer, Sven, Klenin, Konstantin, Sebald, Walter, Hoheisel, Jörg D., Gauer, Christoph, Goychuk, Igor

“…It is well documented that diffusion has generally a strong effect on the binding kinetics in the microtiter plate immunoassays. However, a systematic…”
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Variance of writhe for wormlike DNA rings with excluded volume by Klenin, K V, Vologodskii, A V, Anshelevich, V V, Klishko VYu, Dykhne, A M, Frank-Kamenetskii, M D

“…We have calculated the variance of the equilibrium distribution of a circular wormlike polymer chain over the writhing number, less than (Wr)2 greater than,…”
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A Brownian Dynamics Program for the Simulation of Linear and Circular DNA and Other Wormlike Chain Polyelectrolytes by Klenin, Konstantin, Merlitz, Holger, Langowski, Jörg

“…For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of…”
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Kinetics of Site–Site Interactions in Supercoiled DNA with Bent Sequences by Bussiek, Malte, Klenin, Konstantin, Langowski, Jörg

“…A curved DNA segment is known to adopt a preferred end loop localization in superhelical (sc) DNA and thus may organize the overall conformation of the…”
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Computational Analysis of the Chiral Action of Type II DNA Topoisomerases by Klenin, Konstantin, Langowski, Jörg, Vologodskii, Alexander

“…It was found recently that bacterial type II DNA topoisomerase, topo IV, is much more efficient in relaxing (+) DNA supercoiling than (−) supercoiling. This…”
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Topological characteristics of circular DNA: excluded volume effects by Klenin, K. V., Vologodskii, A. V., Anshelevich, V. V., Dykhne, A. M., Frank-Kamenetskii, M. D.

“…The Monte Carlo method is used to calculate the probability…”
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