arXiv subjects

E. Orlandini

Publications and source records attributed to E. Orlandini.

44 records · Page 3Linked to original sources

arXiv2001

Deciphering the folding kinetics of transmembrane helical proteins

Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely unsolved, key problem in structural biology. Here, we introduce a general model and use computer simulations to study the equilibrium properties and the folding kinetics of a $C_α$-based two helix bundle fragment (comprised of 66 amino-acids) of Bacteriorhodopsin. Various intermediates are identified and their free energy are calculated toghether with the free energy barrier between them. In 40% of folding trajectories, the folding rate is considerably increased by the presence of non-obligatory intermediates acting as traps. In all cases, a substantial portion of the helices is rapidly formed. This initial stage is followed by a long period of consolidation of the helices accompanied by their correct packing within the membrane. Our results provide the framework for understanding the variety of folding pathways of helical transmembrane proteins.

cond-mat.stat-mech↗

arXiv2001

Dynamical scaling of the DNA unzipping transition

We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the force vs temperature plane, which reveals the presence of an interesting re-entrant unzipping transition for low T, these models enable us to characterize the dynamics of the process starting from a non-equilibrium initial condition. The thermal melting of the DNA strands displays a model dependent time evolution. On the contrary, our results suggest that the dynamical mechanism for the unzipping by force is very robust and the scaling behaviour does not depend on the details of the description we adopt.

cond-mat.soft↗

arXiv1999

Simulations of liquid crystal hydrodynamics

We present a lattice Boltzmann algorithm for liquid crystal hydrodynamics. The coupling between the tensor order parameter and the flow is treated consistently allowing investigation of a wide range of non-Newtonian flow behavior. We present results for the effect of hydrodynamics on defect coalescence; of the appearance of the log-rolling and kayaking states in Poiseuille flow; and for banding and coexistence of isotropic and nematic phases under shear.

cond-mat.soft↗

arXiv1999

Adsorption-like Collapse of Diblock Copolymers

A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive MC simulations in two and three dimensions. In the former case, an identification with the statistical geometry of suitable percolation paths allows to predict that the number of contacts between the blocks grows like $N^{9/16}$. In the compact phase the blocks are mixed and, in two dimensions, also zipped, in such a way to form a spiral, double chain structure.

cond-mat.soft↗

arXiv1999

Phase diagram of magnetic polymers

We consider polymers made of magnetic monomers (Ising or Heisenberg-like) in a good solvent. These polymers are modeled as self-avoiding walks on a cubic lattice, and the ferromagnetic interaction between the spins carried by the monomers is short-ranged in space. At low temperature, these polymers undergo a magnetic induced first order collapse transition, that we study at the mean field level. Contrasting with an ordinary $Θ$ point, there is a strong jump in the polymer density, as well as in its magnetization. In the presence of a magnetic field, the collapse temperature increases, while the discontinuities decrease. Beyond a multicritical point, the transition becomes second order and $Θ$-like. Monte Carlo simulations for the Ising case are in qualitative agreement with these results.

cond-mat.stat-mech↗

arXiv1998

Collapse transitions of a periodic hydrophilic hydrophobic chain

We study a single self avoiding hydrophilic hydrophobic polymer chain, through Monte Carlo lattice simulations. The affinity of monomer $i$ for water is characterized by a (scalar) charge $λ_{i}$, and the monomer-water interaction is short-ranged. Assuming incompressibility yields an effective short ranged interaction between monomer pairs $(i,j)$, proportional to $(λ_i+λ_j)$. In this article, we take $λ_i=+1$ (resp. ($λ_i=- 1$)) for hydrophilic (resp. hydrophobic) monomers and consider a chain with (i) an equal number of hydro-philic and -phobic monomers (ii) a periodic distribution of the $λ_{i}$ along the chain, with periodicity $2p$. The simulations are done for various chain lengths $N$, in $d=2$ (square lattice) and $d=3$ (cubic lattice). There is a critical value $p_c(d,N)$ of the periodicity, which distinguishes between different low temperature structures. For $p >p_c$, the ground state corresponds to a macroscopic phase separation between a dense hydrophobic core and hydrophilic loops. For $p <p_c$ (but not too small), one gets a microscopic (finite scale) phase separation, and the ground state corresponds to a chain or network of hydrophobic droplets, coated by hydrophilic monomers. We restrict our study to two extreme cases, $p \sim O(N)$ and $p\sim O(1)$ to illustrate the physics of the various phase transitions. A tentative variational approach is also presented.

cond-mat↗

arXiv1998

Lattice Boltzmann simulations of lamellar and droplet phases

Lattice Boltzmann simulations are used to investigate spinodal decomposition in a two-dimensional binary fluid with equilibrium lamellar and droplet phases. We emphasise the importance of hydrodynamic flow to the phase separation kinetics. For mixtures slightly asymmetric in composition the fluid phase separates into bulk and lamellar phases with the lamellae forming distinctive spiral structures to minimise their elastic energy.

cond-mat.soft↗

arXiv1997

Spinodal decomposition to a lamellar phase: effects of hydrodynamic flow

Results are presented for the kinetics of domain growth of a two-dimensional fluid quenched from a disordered to a lamellar phase. At early times when a Lifshitz-Slyozov mechanism is operative the growth process proceeds logarithmically in time to a frozen state with locked-in defects. However when hydrodynamic modes become important, or the fluid is subjected to shear, the frustration of the system is alleviated and the size and orientation of the lamellae attain their equilibrium values.

cond-mat↗