Related papers: A Rational Method for Probing Macromolecules Disso…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
We describe a method to simulate the dynamics of charged colloidal particles suspended in a liquid containing dissociated ions and salt ions. Regimes of prime current interest are those of large volume fraction of colloids, highly charged…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
Open many-body quantum systems have attracted renewed interest in the context of quantum information science and quantum transport with biological clusters and ultracold atomic gases. The physical relevance in many-particle bosonic systems…
A method of data analysis is proposed for the determination of the carrier recombination processes in optically excited matter measured by time-resolved photoluminescence, differentiating monomolecular, bi-molecular, tri-molecular, and…
Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the…
Background. The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. We demonstrate the accuracy and effectiveness of a Lagrangian particle-based…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
Understanding mechanisms for energy dissipation from nanoparticles in contact with large samples is a central problem in describing friction microscopically. Calculation of the reduced density matrix appears to be the most suitable metho to…
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…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
We analyze the response of molecular adhesion complexes to increasing pulling forces (dynamic force spectroscopy) when dissociation can occur along either one of two alternative trajectories in the underlying multidimensional energy…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device. The importance of orientation dependent interactions…
An ongoing problem in the study of a classical many-body system is the characterization of its equilibrium behaviour by theory or numerical simulation. For purely repulsive particles, locating the melting line in the pressure-temperature…
The decay process of the schematic one-dimensional three-body system is considered. A time-dependent approach is used in combination with a one-dimensional three-body model, which is composed of a heavier core nucleus and two nucleons, with…
The spontaneous disentanglement hypothesis is motivated by some outstanding issues in standard quantum mechanics, including the problem of quantum measurement. The current study compares between some possible methods that can be used to…
We investigate the quantum many-body dynamics of dissociation of a Bose-Einstein condensate of molecular dimers into pairs of constituent bosonic atoms and analyze the resulting atom-atom correlations. The quantum fields of both the…
We study the non-equilibrium statistical mechanics of a system of freely moving particles, in which binary encounters lead either to an elastic collision or to the disappearance of the pair. Such a system of {\em ballistic annihilation}…