Journal of Physics A: Mathematical and Theoretical
We report on non-equilibrium phase transitions in the driven lattice gas model totally asymmetric... more We report on non-equilibrium phase transitions in the driven lattice gas model totally asymmetric exclusion processes caused by nearest-neighbor (NN) repulsions between particles, ɛ > 0, employing extensive Monte Carlo simulations and mean-field calculations. The diagra of phase regimes has five different regimes which are separated by distinct boundaries. We discuss the density of particles and the current which depend differently in the various regimes on the system’s entry and exit rates of particles, α and β, respectively. The steady state can be described by quasi-particles called ‘soft dimerons’, where each dimeron consists of a particle dragging an empty NN site on its left. The asymptotic state of dimerons at ε → ∞ is equivalent to the state of hard dimers at ɛ = 0. Since the model is a uni-directional fluid, it has an internal hydrodynamic pressure which increases with increasing inter-particle repulsion ɛ. This leads to a collective effect which causes phase transitions...
Computational and Theoretical Polymer Science, 1997
Small anisotropic networks changing periodically or randomly their internal structures perform a ... more Small anisotropic networks changing periodically or randomly their internal structures perform a unidirectional migration. Implications of such contractile networks for cell cytoskeletons are discussed.
The present review reports on recent progress in modeling and simulation of biological ion channe... more The present review reports on recent progress in modeling and simulation of biological ion channels and proton pumps. In particular, we describe the current approaches and results concerning permeation and selectivity of ion channels. This is demonstrated mainly at the example of a potassium ion channel. In the case of proton pumping across lipid membranes we report on recent results from computer simulation of bacteriorhodopsin. The distribution of internal water and the structure and dynamics of hydrogen-bonded networks inside bacteriorhodopsin are discussed.
A self-avoiding polymer embedded in a two-dimensional quenched random medium consisting of random... more A self-avoiding polymer embedded in a two-dimensional quenched random medium consisting of randomly distributed attractive sites has been studied using Monte Carlo methods. It is shown that at a critical temperature the adsorption energy exhibits a sharp transition to a localized state. The transition is characterized by a discontinuity of the adsorption energy at the critical point. The radius of gyration of the chain remains essentially unaffected by the disorder with respect to the chain length dependency. However, there is some evidence that at the critical point the size of the polymer starts to increase with decreasing temperature. Formulas for energy and critical temperature are suggested.
We have investigated the shape, size, and motility of a minimal model of an adherent biological c... more We have investigated the shape, size, and motility of a minimal model of an adherent biological cell using the Monte Carlo method. The cell is modeled as a two dimensional ring polymer on the square lattice enclosing continuously polymerizing and depolymerizing actin networks. Our lattice model is an approximate representation of a real cell at a resolution of one actin molecule, 5 nm. The polymerization kinetics for the actin network are controlled by appropriate reaction probabilities which correspond to the correct experimental reaction rates. Using the simulation data we establish various scaling laws relating the size of the model cell to the concentration of polymerized and unpolymerized actin molecules and the length of the enclosing membrane. The computed drift velocities, which characterize the motility of the cell, exhibit a maximum at a certain fraction of polymerized actin which agrees with physiological fractions observed in experiments. The appearance of the maximum is...
Advances in experimental medicine and biology, 2014
Membrane proteins play crucial roles in a range of biological processes. High resolution structur... more Membrane proteins play crucial roles in a range of biological processes. High resolution structures provide insights into the functional mechanisms of membrane proteins, but detailed biophysical characterization of membrane proteins is difficult. Complementary to experimental techniques, molecular dynamics simulations is a powerful tool in providing more complete description of the dynamics and energetics of membrane proteins with high spatial-temporal resolution. In this chapter, we provide a survey of the current methods and technique issues for setting up and running simulations of membrane proteins. The recent progress in applying simulations to understanding various biophysical properties of membrane proteins is outlined.
This review describes some recent theories and simulations of mesoscopic and microscopic models o... more This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins.
Journal of Physics A: Mathematical and Theoretical
We report on non-equilibrium phase transitions in the driven lattice gas model totally asymmetric... more We report on non-equilibrium phase transitions in the driven lattice gas model totally asymmetric exclusion processes caused by nearest-neighbor (NN) repulsions between particles, ɛ > 0, employing extensive Monte Carlo simulations and mean-field calculations. The diagra of phase regimes has five different regimes which are separated by distinct boundaries. We discuss the density of particles and the current which depend differently in the various regimes on the system’s entry and exit rates of particles, α and β, respectively. The steady state can be described by quasi-particles called ‘soft dimerons’, where each dimeron consists of a particle dragging an empty NN site on its left. The asymptotic state of dimerons at ε → ∞ is equivalent to the state of hard dimers at ɛ = 0. Since the model is a uni-directional fluid, it has an internal hydrodynamic pressure which increases with increasing inter-particle repulsion ɛ. This leads to a collective effect which causes phase transitions...
Computational and Theoretical Polymer Science, 1997
Small anisotropic networks changing periodically or randomly their internal structures perform a ... more Small anisotropic networks changing periodically or randomly their internal structures perform a unidirectional migration. Implications of such contractile networks for cell cytoskeletons are discussed.
The present review reports on recent progress in modeling and simulation of biological ion channe... more The present review reports on recent progress in modeling and simulation of biological ion channels and proton pumps. In particular, we describe the current approaches and results concerning permeation and selectivity of ion channels. This is demonstrated mainly at the example of a potassium ion channel. In the case of proton pumping across lipid membranes we report on recent results from computer simulation of bacteriorhodopsin. The distribution of internal water and the structure and dynamics of hydrogen-bonded networks inside bacteriorhodopsin are discussed.
A self-avoiding polymer embedded in a two-dimensional quenched random medium consisting of random... more A self-avoiding polymer embedded in a two-dimensional quenched random medium consisting of randomly distributed attractive sites has been studied using Monte Carlo methods. It is shown that at a critical temperature the adsorption energy exhibits a sharp transition to a localized state. The transition is characterized by a discontinuity of the adsorption energy at the critical point. The radius of gyration of the chain remains essentially unaffected by the disorder with respect to the chain length dependency. However, there is some evidence that at the critical point the size of the polymer starts to increase with decreasing temperature. Formulas for energy and critical temperature are suggested.
We have investigated the shape, size, and motility of a minimal model of an adherent biological c... more We have investigated the shape, size, and motility of a minimal model of an adherent biological cell using the Monte Carlo method. The cell is modeled as a two dimensional ring polymer on the square lattice enclosing continuously polymerizing and depolymerizing actin networks. Our lattice model is an approximate representation of a real cell at a resolution of one actin molecule, 5 nm. The polymerization kinetics for the actin network are controlled by appropriate reaction probabilities which correspond to the correct experimental reaction rates. Using the simulation data we establish various scaling laws relating the size of the model cell to the concentration of polymerized and unpolymerized actin molecules and the length of the enclosing membrane. The computed drift velocities, which characterize the motility of the cell, exhibit a maximum at a certain fraction of polymerized actin which agrees with physiological fractions observed in experiments. The appearance of the maximum is...
Advances in experimental medicine and biology, 2014
Membrane proteins play crucial roles in a range of biological processes. High resolution structur... more Membrane proteins play crucial roles in a range of biological processes. High resolution structures provide insights into the functional mechanisms of membrane proteins, but detailed biophysical characterization of membrane proteins is difficult. Complementary to experimental techniques, molecular dynamics simulations is a powerful tool in providing more complete description of the dynamics and energetics of membrane proteins with high spatial-temporal resolution. In this chapter, we provide a survey of the current methods and technique issues for setting up and running simulations of membrane proteins. The recent progress in applying simulations to understanding various biophysical properties of membrane proteins is outlined.
This review describes some recent theories and simulations of mesoscopic and microscopic models o... more This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins.
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Papers by Artur Baumgaertner