Effect of grafting on the binding transition of two flexible polymers

We investigate the binding transition of two flexible polymers grafted to a steric surface with closeby end points. While free polymers show a discontinuous transition, grafting to a steric flat surface leads to a continuous binding transition. This is supported by results from Metropolis and parallel multicanonical simulations. A combination of canonical and microcanonical analyses reveals that the change in transition order can be understood in terms of the reduced translational entropy of the unbound high-temperature phase upon grafting.Comment: 10 pages, 6 figures, submitted to Eur. Phys. J Spec. Topic

Studies of an Off-Lattice Model for Protein Folding: Sequence Dependence and Improved Sampling at Finite Temperature

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level spectra of chains with different types of behavior are compared. Furthermore, we use this model as a testbed for two improved Monte Carlo algorithms. Both algorithms are based on letting some parameter of the model become a dynamical variable; one of the algorithms uses a fluctuating temperature and the other a fluctuating monomer sequence. We find that by these algorithms one gains large factors in efficiency in comparison with conventional methods.Comment: 17 pages, 9 Postscript figures. Combined with chem-ph/950500

From Particle Condensation to Polymer Aggregation: Phase Transitions and Structural Phases in Mesoscopic Systems: From Particle Condensation to Polymer Aggregation:Phase Transitions and Structural Phases in Mesoscopic Systems

Die vorliegende Arbeit befasst sich mit den Gleichgewichtseigenschaften und Phasenübergängen in verdünnten Teilchen- und Polymersystemen, mit einem Fokus auf Teilchenkondensation und Polymeraggregation. Dazu werden sowohl analytische Argumente als auch hochentwickelte Monte Carlo Simulationen verwendet. Um die in dieser Arbeit erreichten Systemgrößen zu simulieren, wurde eine parallele Version der multikanonischen Methode entwickelt. Die Leistungsfähigkeit dieser Erweiterung wird an mehreren relevanten Beispielen demonstriert. Um Teilchenkondensation und Polymeraggregation in finiten Systemen und in geometrisch beschränkten Strukturen besser zu verstehen, wird der Einfluss von verschiedenen Parametern auf die jeweiligen Übergange untersucht. Dies beinhaltet unter anderem die Systemgröße und Dichte, sowie im Speziellen für semiflexible Polymere deren Steifigkeit. Betrachtet werden sowohl kanonische Observablen (Energie, Tropfen- bzw. Aggregatgröße, etc.) mit der dazugehörigen Übergangstemperatur und -breite, als auch eine mikrokanonische Analyse sowie die Barrieren der Freien Energie. Für semiflexible Polymere wird insbesondere der Einfluss von Steifigkeit auf die resultierende Struktur der Aggregate untersucht, die von amorphen Kugeln für flexible Polymere bis hin zu verdrehten Bündeln für steifere Polymere reichen. Ein weiterer Fokus liegt auf der Untersuchung von Übereinstimmungen zwischen den generischen Mechanismen in Kondensation und Aggregation: dem Übergang zwischen einer homogenen Phase und einer inhomogenen (gemischten) Phase. Auf diesem Niveau kann man Polymeraggregation als Kondensation von ausgedehnten Objekten verstehen. Dies zeigt sich vor allem in dem Skalierungsverhalten von kanonischen und mikrokanonischen Observablen, insbesondere an einem unerwarteten aber konsistenten Bereich für mittelgroße (mesoskopische) Systemgrößen

Extended Ensemble Molecular Dynamics for Thermodynamics of Phases

The first-order phase transitions and related thermodynamics properties are primary concerns of materials sciences and engineering. In traditional atomistic simulations, the phase transitions and the estimation of their thermodynamic properties are challenging tasks because the trajectories get trapped in local minima close to the initial states. In this study, we investigate various extended ensemble molecular dynamics (MD) methods based on the multicanonical ensemble method using the Wang-Landau (WL) approach. We performed multibaric-multithermal (MBMT) method to fluid phase, gas-liquid transition, and liquid-solid transition of the Lennard-Jones (LJ) system. The derived thermodynamic properties of the fluid phase and the gas-liquid transition from the MBMT agree well with the previously reported equation of states (EOSs). However, the MBMT cannot correctly predict the liquid-solid transition. The multiorder-multithermal (MOMT) ensemble shows significantly enhanced sampling between liquid and solid states with an accurate estimation of transition temperatures. We further investigated the dynamics of each system based on their free energy shapes, providing fundamental insights for their sampling behaviors. This study guides the prediction of broader crystalline materials, e.g., alloys, for their phases and thermodynamic properties from atomistic modeling

Minimal model for the secondary structures and conformational conversions in proteins

Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced off-lattice model that can express α-helix and β-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a β-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both α-helix and β-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of β-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method an effcient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between α-helix and β-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined