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  • 1
    Keywords: Germany ; SYSTEM ; SYSTEMS ; TIME ; DNA ; DYNAMICS ; SIMULATION ; MOLECULE ; LENGTH ; KINETICS ; CHAIN ; CONTROLLED INTRACHAIN REACTIONS ; CYCLIZATION DYNAMICS ; DIFFUSION-CONTROLLED REACTIONS ; FLEXIBLE POLYMERS ; NON-SIMPLE MOLECULES ; REACTION-RATES ; RENORMALIZATION-GROUP THEORY ; SUPERCOILED DNA
    Abstract: By the traditional approach to the Brownian dynamics simulations of intrachain reactions of polymers, the initial chain conformation is sampled from the equilibrium distribution. A dynamic trajectory is carried out until a "collision" of the reactive groups takes place, i.e., the distance between their centers becomes less that a certain reaction radius. The average length of the trajectory is equal to the mean time tau(F) of a diffusion-controlled reaction. In this work we propose another computational scheme. The trajectory begins at the instant of collision and is carried out until the chain is relaxed. The length of the trajectory has the order of the relaxation time tau(rel) of the distance between the reactive groups. For polymer systems with tau(rel)much greater than tau(F), this scheme allows the computation of tau(F) with considerable gain in computational time. Using the present approach, we calculated the mean time of DNA cyclization for the molecule length in the range from 50 to 500 nm. (C) 2004 American Institute of Physics
    Type of Publication: Journal article published
    PubMed ID: 15332931
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  • 2
    Keywords: AB-INITIO ; ENERGIES ; MODEL ; SYSTEM ; ENERGY ; REGION ; SURFACE ; C2H MOLECULE ; COLLISIONS ; ELECTRONIC STATES ; POTENTIAL-ENERGY SURFACES ; GEOMETRIC PHASE ; MATRIX ; NONADIABATIC COUPLING TERMS ; POLYATOMIC-MOLECULES ; BIMOLECULAR REACTIVE SYSTEMS ; INITIO CONICAL INTERSECTIONS
    Abstract: In this article we consider the electronic diabatic presentation of a two-state system with the aim of earning insight regarding the distribution of conical intersections in a given region. In this process we revealed explicit relationship between the diabatic potentials and the locations of conical intersections. The study is accompanied with numerical examples as worked out for a model and ab initio potential energy surfaces of the Na+H-2 system. (C) 2004 American Institute of Physics
    Type of Publication: Journal article published
    PubMed ID: 15268400
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  • 3
    Keywords: SIMULATIONS ; SYSTEM ; SYSTEMS ; SITES ; PROTEIN ; PROTEINS ; TIME ; SIMULATION ; DNA-BINDING ; PARAMETERS ; DIFFUSION ; SIZE
    Abstract: The recently introduced method of excess collisions to estimate reaction times of protein-DNA systems in the presence of facilitated diffusion ("sliding") requires a cell of full system size. This bottleneck is avoided with a modification, by which a set of empirical parameters is calibrated using numerical simulations of a small test system. Once this is done, reaction times for systems of arbitrary dimensions are derived by extrapolation. It is shown that at physiological sliding lengths a test system of the order of 100 nm radius suffices to extract accurate reaction times for realistic cell dimensions. The achieved speedup, when compared to explicit simulations of the reaction process, is increasing in third order of the extrapolated radius of the cell
    Type of Publication: Journal article published
    PubMed ID: 16863332
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  • 4
    Keywords: CELL ; Germany ; IN-VIVO ; MODEL ; NETWORKS ; VOLUME ; PROTEIN ; PROTEINS ; DNA ; DYNAMICS ; PARTICLES ; TRANSPORT ; NO ; CHROMATIN ; LIVING CELLS ; DIFFUSION ; fluorescence correlation spectroscopy ; molecular ; CHAIN ; methods ; ANOMALOUS DIFFUSION ; USA ; CHROMATIN FIBER ; NUCLEOSOME CORE PARTICLES
    Abstract: In this paper, a lattice model for the diffusional transport of chromatin-binding particles in the interphase cell nucleus is proposed. Sliding effects are studied in dense networks of chromatin fibers created by three different methods: Randomly distributed, noninterconnected obstacles, a random walk chain model with an attractive step potential, and a self-avoiding random walk chain model with a hard repulsive core and attractive surroundings. By comparing a discrete and continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter the diffusion of chromatin-binding particles. The influence of conformational properties of the fiber network on the particle sliding is investigated in detail while varying occupation volume, sliding probability, chain length, and persistence length. It is observed that adjacency of the monomers, the excluded volume effect incorporated in the self-avoiding random walk model, and the persistence length affect the chromatin-binding particle diffusion. It is demonstrated that sliding particles sense local chain structures. When plotting the diffusion coefficient as a function of the accessible volume for diffusing particles, the data fall onto master curves depending on the persistence length. However, once intersegment transfer is involved, chromatin-binding proteins no longer perceive local chain structures. (C) 2008 American Institute of Physics
    Type of Publication: Journal article published
    PubMed ID: 18433282
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  • 5
    Keywords: CELLS ; ANOMALOUS DIFFUSION ; FRACTIONAL BROWNIAN-MOTION ; OBSTACLES
    Abstract: We propose a kinetic Monte Carlo method for the simulation of subdiffusive random walks on a cartesian lattice. The random walkers are subject to viscoelastic forces which we compute from their individual trajectories via the fractional Langevin equation. At every step the walkers move by one lattice unit, which makes them differ essentially from continuous time random walks, where the subdiffusive behavior is induced by random waiting. To enable computationally inexpensive simulations with n-step memories, we use an approximation of the memory and the memory kernel functions with a complexity O(log n). Eventual discretization and approximation artifacts are compensated with numerical adjustments of the memory kernel functions. We verify with a number of analyses that this new method provides binary fractional random walks that are fully consistent with the theory of fractional brownian motion.
    Type of Publication: Journal article published
    PubMed ID: 22897262
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  • 6
    Keywords: EXCHANGE ; FORMALISM ; FRACTIONALLY OCCUPIED STATES ; CORRECT ASYMPTOTIC-BEHAVIOR ; DENSITY-FUNCTIONAL THEORY ; INTEGER DISCONTINUITY
    Type of Publication: Journal article published
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  • 7
    Keywords: AB-INITIO ; SYSTEM ; LINES ; FORM ; ELEMENTS ; TRANSFORMATION ; C2H MOLECULE ; COLLISIONS ; DIABATIC REPRESENTATIONS ; ELECTRONIC STATES ; H+H-2 SYSTEM ; MOLECULAR-SYSTEMS ; NONADIABATIC COUPLING MATRIX ; POTENTIAL-ENERGY SURFACES
    Abstract: This article presents a detailed study of the various conical intersections (ci) related to the four lower states of the title system. The approach is based on freezing the positions of the two hydrogens (the distance between them is assumed to be 2.18 a.u. throughout the present study) and allowing the sodium atom to move, undisturbed, to reveal the locations of the ci's as well as the spatial distribution of their nonadiabatic coupling terms (NACTs). We found altogether seven ci's-one between the ground state and the first excited state, thus a (1,2) ci, two between the first excited state and the second excited state thus (2,3) ci's, and the last four are between the second excited state and the third excited state, thus (3,4) ci's. It was established that the (1,2) ci is a C-2v ci located on the symmetry line orthogonal to the HH axis, the (2,3) ci's are C-2v ci's located on the HH axis (at symmetric positions) and, out of the four (3,4) ci's, two are C-2v ci's located on the above-mentioned symmetry line, and the other two are C-s ci's located on both sides of this symmetry line. It was revealed that all seven ci's are of the elliptic type [Chem. Phys. Lett. 354, 243(2002)], namely their NACTs are concentrated along straight lines-five of them are concentrated along lines parallel to the HH axis and two along the symmetry line vertical to the HH axis. Particular attention is given to two-state, three-state, and four-state quantization. From a practical point of view this study revealed the fact that in general, the two lower states of the Na+H-2 system form an isolated group of states, which implies that the two-state system can be diabatized. (C) 2003 American Institute of Physics
    Type of Publication: Journal article published
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  • 8
    Keywords: AB-INITIO ; SYSTEM ; TIME ; MOLECULE ; NUMBER ; LINE ; SELECTION ; STATES ; EXCITED-STATES ; COLLISIONS ; H+H-2 SYSTEM ; POTENTIAL-ENERGY SURFACES ; INTEGRATION ; CONICAL INTERSECTIONS ; MATRIX ; HYDROGEN ; excited states ; DIABATIC TRANSFORMATION ; QUANTUM DYNAMICS
    Abstract: This paper is devoted to a specific difficulty related to the electronic nonadiabatic coupling terms (NACT), namely, how to determine correctly their signs. It is well known that correct NACTs, including their signs, are crucial for any numerical treatment of the nuclear Schrodinger equation [see, i.e., A. Kuppermaan and R. Abrol, Adv. Chem. Phys. 124, 283 (2003)]. In most cases the derivation of the correct sign of the nonadiabatic coupling matrix (NACM) is done employing various continuity procedures. However, there are cases where these procedures do not suffice and for these cases we suggest to apply an additional procedure based on a mathematical lemma which asserts that the exponentiated line integral which yields the D matrix is invariant with respect to the initial point of the integration [M. Baer, J. Phys. Chem. A 104, 3181 (2000)]. In the numerical study we apply this lemma to determine the signs of the 3x3 NACM elements for the three excited states of the {H-2,O} system (some of these NACTs are presented here for the first time). It turns out that the ab initio treatment yields results from which one can form eight different 3x3 NACMs. However the application of this lemma (which does not require any significant additional numerical effort) reduces this number to two. The final selection is done by an enhanced numerical study which requires more accurate calculations. (C) 2005 American Institute of Physics
    Type of Publication: Journal article published
    PubMed ID: 15847457
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  • 9
    Keywords: SIMULATIONS ; SYSTEM ; SITE ; PROTEIN ; PROTEINS ; SIMULATION ; BINDING ; ASSOCIATION ; RATES ; DNA-BINDING ; DIFFUSION ; SIZE ; BINDING-SITE ; physics
    Abstract: In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing modes, a free diffusion and a DNA-sliding mode, to search for its specific binding site in the center of the cell. There is no need for a straightforward simulation of this process. Instead, an alternative and exact approach is shown to be essentially faster than explicit random walk simulations. The speed-up of this novel simulation technique is rapidly growing with system size. (c) 2006 American Institute of Physics
    Type of Publication: Journal article published
    PubMed ID: 16613478
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  • 10
    Keywords: SPECTRA ; STATES ; molecular ; CHEMISTRY ; FEATURES ; POTENTIALS ; NANOPARTICLES ; USA ; PEOPLE ; CIRCULATION ; LUMINESCENCE ; ELECTRONIC-PROPERTIES ; NANOCLUSTERS ; NANOCRYSTALS ; QUANTUM DOTS ; POROUS SILICON ; DEVICE
    Abstract: Surface functionalization is a critical step for Si nanocrystals being used as biological probes and sensors. Using density-functional tight-binding calculations, we systematically investigate the optical properties of silicon quantum dots (SiQDs) with various termination groups, including H, CH3, NH2, SH, and OH. Our calculations reveal that capping SiQDs with alkyl group (-Si-C-) induces minimal changes in the optical spectra, while covering the surface with NH2, SH, and OH results in evident changes compared to hydrogenated SiQDs. The structural deformations and electronic property changes due to surface passivation were shown to be responsible for the above-described features. Interestingly, we find that the optical properties of SiQDs can be controlled by varying the S coverage on the surface. This tuning effect may have important implications in device fabrications. (c) 2008 American Institute of Physics
    Type of Publication: Journal article published
    PubMed ID: 18601372
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