|
| |
|
| |
|
| |
|
|
Energetics of diffusion in time-dependent parabolic potential.
Škvára, Jan ; Chvosta, Petr (advisor) ; Netočný, Karel (referee)
In this thesis we are going to study the dynamics and energetics of the dif- fusion of a Brownian particle in a time-dependent parabolic potential. Our central quantity is a random variable corresponding to the work done on the particle due to the time dependency of the potential. We present new exact analytical ex- pression for the probability density function for the work variable in a situation, where the potential is piecewise constant in the time variable. Furthermore, this result is used to develop a hierarchy of approximations which yield the density function for an arbitrary time-dependent parabolic potential. 1
|
|
|
Stochastická dynamika bublin v DNA
Kaiser, Vojtěch ; Novotný, Tomáš (advisor) ; Chvosta, Petr (referee)
Název práce: Stochastická dynamika bublin v DNA Autor: Bc. Vojtěch Kaiser Katedra: Katedra fyziky kondenzovaných látek Vedoucí diplomové práce: RNDr. Tomáš Novotný, Ph.D., Katedra fyziky kondenzovaných látek Abstrakt: Bubliny v DNA jsou místa, kde se vlivem tepelných či torsních vlivů otevírá dvojšroubovice DNA. Tyto bubliny jsou považovány za důležité pro termodynamiku DNA [56] a biologické procesy s DNA spojené [23,40,43,49]. V článcích [38, 39] byla řešena stochastická dynamika bublin v DNA na zá- kladě Polandova-Scheragova modelu a získány analytické výsledky při tep- lotě denaturace DNA a pro asymptotiku dlouhých časů, zvláště pro hustotu pravděpodobnosti času setkání konců bubliny. V této práci navazujeme na tyto výsledky a počítáme celkový tvar této hustoty pravděpodobností s vy- užitím numerické inverse analytických vztahů v Laplacově obraze. Dále po- čítáme hustotu pravděpodobnosti místa setkání konců bubliny. Odpovídající výsledky jsou numericky spočteny v případě molekul DNA konečné délky. Zachycování bubliny v oblastech bohatých na AT páry je modelováno jako subdifusivní systém dle článku [42] a jsou počítány stejné veličiny jako pro difusivní model. V závěru diskutujeme tyto výsledky a možnost jejich experi- mentálního ověření. Klíčová slova: bubliny v DNA,...
|
|
| |
|
|
Brownian motion in logarithmic potential
Berestneva, Ekaterina ; Ryabov, Artem (advisor) ; Chvosta, Petr (referee)
In this thesis we study first-passage properties of a Brownian particle diffusing under the action of logarithmic potential field U(x, t) = g(t) log(x). The main part of this thesis is de- voted to the case of time-dependent potential strength g(t). To obtain the corresponding survival probability, one may try to solve the Fokker-Planck equation. However, its exact solution for the time-dependent potential is yet unknown. In this work we propose a simple asymptotic theory which yields the long-time behaviour of the survival probability and the moments of the particle position. The survival probability exhibits a rather varied behaviour for different functions g(t). We identify three regimes of asymptotic decay: the regular regime, the marginal regime and the regime of enhanced absorption. We also address the question of how will the derived first-passage properties of Brownian motion change when the absorbing boundary is not exactly at the origin. 1
|
|
|
Stochastic dynamics and energetics of biomolecular systems
Ryabov, Artem ; Chvosta, Petr (advisor) ; Novotný, Tomáš (referee) ; Papáček, Štěpán (referee)
Title: Stochastic dynamics and energetics of biomolecular systems Author: Artem Ryabov Department: Department of Macromolecular Physics Supervisor: prof. RNDr. Petr Chvosta, CSc., Department of Macromolecular Physics Abstract: The thesis comprises exactly solvable models from non-equilibrium statistical physics. First, we focus on a single-file diffusion, the diffusion of particles in narrow channel where particles cannot pass each other. After a brief review, we discuss open single-file systems with absorbing boundaries. Emphasis is put on an interplay of absorption process at the boundaries and inter-particle entropic repulsion and how these two aspects affect the dynam- ics of a given tagged particle. A starting point of the discussions is the exact distribution for the particle displacement derived by order-statistics argu- ments. The second part of the thesis is devoted to stochastic thermodynam- ics. In particular, we present an exactly solvable model, which describes a Brownian particle diffusing in a time-dependent anharmonic potential. The potential has a harmonic component with a time-dependent force constant and a time-independent repulsive logarithmic barrier at the origin. For a particular choice of the driving protocol, the exact work characteristic func- tion is obtained. An asymptotic analysis of...
|
|
|
Symmetries of transition times in complex biophysical systems
Voráč, David ; Ryabov, Artem (advisor) ; Chvosta, Petr (referee)
Conformational changes of biomolecules can be described as Markov processes on net- works of discrete states representing minima of free energy landscapes. Network states for several types of membrane proteins and molecular motors are linked into cycles, and their reaction coordinates (represented by a "particle") jump between the cycle states predominantly in one direction with rare backward jumps occurring due to thermal fluc- tuations. Assuming that interactions of the particle with other degrees of freedom (other particles) cannot be neglected, we study times that it takes to complete one cycle. In par- ticular, we compare mean times of cycle completion in and against the bias direction and show that they satisfy the universal inequality: Cycle-completion times in bias direction are never shorter than the ones against the bias. We discuss how the times depend on the interaction strength, cycle topology, quenched disorder, number of interacting par- ticles, and check validity of our findings for two-dimensional models with canonical and grand-canonical particle reservoirs.
|
|
|
Energetics of diffusion in time-dependent parabolic potential.
Škvára, Jan ; Chvosta, Petr (advisor) ; Netočný, Karel (referee)
In this thesis we are going to study the dynamics and energetics of the dif- fusion of a Brownian particle in a time-dependent parabolic potential. Our central quantity is a random variable corresponding to the work done on the particle due to the time dependency of the potential. We present new exact analytical ex- pression for the probability density function for the work variable in a situation, where the potential is piecewise constant in the time variable. Furthermore, this result is used to develop a hierarchy of approximations which yield the density function for an arbitrary time-dependent parabolic potential. 1
|
guest ::
RSS feed.