Cooperative molecular motors moving back and forth (2009)
Gillo, David, Gur, Barak, Bernheim-Groswasser, Anne, Farago, Oded
We use a two-state ratchet model to study the cooperative bidirectional motion of molecular motors on cytoskeletal tracks with randomly alternating polarities. Our model is based on a previously...
Gilboa, Barak, Gillo, David, Farago, Oded, Bernheim-Groswasser, Anne
The cooperative action of many molecular motors is essential for dynamic processes such as cell motility and mitosis. This action can be studied by using motility assays in which the motion of...
Membrane fluctuations near a plane rigid surface (2008)
We use analytical calculations and Monte Carlo simulations to determine the thermal fluctuation spectrum of a membrane patch of a few tens of nanometer in size, whose corners are located at a fixed...
Mode excitation Monte Carlo simulations of mesoscopically large membranes (2008)
Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is...
Farago, Oded, Ewert, Kai, Ahmad, Ayesha, Evans, Heather M., Gr\onbech-Jensen, Niels, Safinya, Cyrus R.
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs),...
Directed chaotic motion in a periodic potential Abstract (2008)
We study the motion of a classical particle in an in nite, one-dimensional, sequence of equidistant potential barriers, whose position and height oscillate periodically. If these oscillations are...
Computational and Analytical Modeling of Cationic Lipid-DNA Complexes (2006)
Farago, Oded, Grønbech-Jensen, Niels
We present a theoretical study of the physical properties of cationic lipid-DNA (CL-DNA) complexes - a promising synthetically based nonviral carrier of DNA for gene therapy. The study is based on a...
Meso-scale computer modeling of lipid-DNA complexes for gene therapy (2005)
Farago, Oded, Grønbech-Jensen, Niels, Pincus, Philip
We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale...
Pore formation in fluctuating membranes (2004)
Farago, Oded, Santangelo, Christian D.
We study the nucleation of a single pore in a fluctuating lipid membrane, specifically taking into account the membrane fluctuations, as well as the shape fluctuations of the pore. For large enough...
Membrane fluctuations around inclusions (2003)
Santangelo, Christian D., Farago, Oded
The free energy of inserting a protein into a membrane is determined by considering the variation in the spectrum of thermal fluctuations in response to the presence of a rigid inclusion. Both...
The Effect of Thermal Fluctuations on Schulman Area Elasticity (2003)
We study the elastic properties of a two-dimensional fluctuating surface whose area density is allowed to deviate from its optimal (Schulman) value. The behavior of such a surface is determined by an...
Statistical mechanics of bilayer membrane with a fixed projected area (2003)
The equilibrium and fluctuation methods for determining the surface tension, $\sigma$, and bending modulus, $\kappa$, of a bilayer membrane with a fixed projected area are discussed. In the...
"Water-free" computer model for fluid bilayer membranes (2003)
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair...
Solute Effects on the Helix-Coil Transition (2002)
We discuss the effects of the solvent composition on the helix-coil transition of a polypeptide chain. We use a simple model to demonstrate that improving the hydrogen-bonding ability of the solvent...
Pulling Knotted Polymers (2002)
Farago, Oded, Kantor, Yacov, Kardar, Mehran
We compare Monte Carlo simulations of knotted and unknotted polymers whose ends are connected to two parallel walls. The force $f$ exerted on the polymer is measured as a function of the separation...
Entropic Elasticity at the Sol-Gel Transition (2001)
The sol-gel transition is studied in two purely entropic models consisting of hard spheres in continuous three-dimensional space, with a fraction $p$ of nearest neighbor spheres tethered by...
Entropic Elasticity of Phantom Percolation Networks (2000)
A new method is used to measure the stress and elastic constants of purely entropic phantom networks, in which a fraction $p$ of neighbors are tethered by inextensible bonds. We find that close to...
Elasticity of Gaussian and nearly-Gaussian phantom networks (2000)
We study the elastic properties of phantom networks of Gaussian and nearly-Gaussian springs. We show that the stress tensor of a Gaussian network coincides with the conductivity tensor of an...
The Elastic Behavior of Entropic "Fisherman's Net" (2000)
A new formalism is used for a Monte Carlo determination of the elastic constants of a two-dimensional net of fixed connectivity. The net is composed of point-like atoms each of which is tethered to...
Pseudo-boundaries in discontinuous 2-dimensional maps (1997)
It is known that Kolmogorov-Arnold-Moser boundaries appear in sufficiently smooth 2-dimensional area-preserving maps. When such boundaries are destroyed, they become pseudo-boundaries. We show that...
Pseudo-boundaries in discontinuous two-dimensional maps (1997)
Abstract. Kolmogorov–Arnold–Moser boundaries appear in sufficiently smooth twodimensional area-preserving maps. When such boundaries are destroyed, they become pseudoboundaries. We show that...
Computational and Analytical Modeling of Cationic Lipid-DNA Complexes
Farago, Oded, Grønbech-Jensen, Niels
We present a theoretical study of the physical properties of cationic lipid-DNA (CL-DNA) complexes—a promising synthetically based nonviral carrier of DNA for gene therapy. The study is based on a...
Transitions between Distinct Compaction Regimes in Complexes of Multivalent Cationic Lipids and DNA
Farago, Oded, Ewert, Kai, Ahmad, Ayesha, Evans, Heather M., Grønbech-Jensen, Niels, Safinya, Cyrus R.
Cationic lipids (CLs) have found widespread use as nonviral gene carriers (vectors), including applications in clinical trials of gene therapy. However, their observed transfection efficiencies (TEs)...